Antimicrobial resistance among producers and non-producers of extended spectrum beta-lactamases in urinary isolates at a tertiary Hospital in Tanzania

<p>Abstract</p> <p>Background</p> <p>Published data on the existence and magnitude of extended spectrum beta-lactamase (ESBL) production in urinary pathogens in local setting is limited. The aim of the present study was to determine the prevalence of antimicrobial resistance and ESBL production among <it>Escherichia coli </it>and <it>Klebsiella spp </it>from urine samples in a tertiary hospital. This was a cross sectional study conducted at Muhimbili National Hospital in Dar es Salaam, Tanzania.</p> <p>Findings</p> <p>A total of 270 <it>E.coli </it>and <it>Klebsiella spp </it>urinary pathogens from children and adults isolated from January to March 2010 were included in the study. <it>E. coli </it>and <it>Klebsiella spp </it>isolates were tested for antimicrobial susceptibility by the Clinical and Laboratory Standard Institute's disc diffusion method. These isolates were further screened for ESBL phenotype using cefotaxime and ceftazidime discs. Isolates with reduced sensitivity were confirmed using ESBL E-test strips. Of 270 isolates, 138 (51.1%) were <it>E. coli </it>and 132 (48.9%) were <it>Klebsiella spp</it>. ESBL was detected in 122 (45.2%) of all the isolates. ESBL- producing <it>E. coli </it>strains were significantly more resistance to cotrimoxazole (90.7%), ciprofloxacin (46.3%) and nalidixic acid (61.6%) than strains that did not produce ESBL (p < 0.05). Similarly, ESBL- producing <it>Klebsiella spp </it>strains were significantly more resistance to cotrimoxazole (92.6%), ciprofloxacin (25.0%), nalidixic acid (66.2%), and gentamicin (38.2%) than strains that did not produce ESBL (P < 0.05). Multi-drug resistance was found to be significantly (<it>P </it>< 0.05) more in ESBL producing isolates (90.5%) than non ESBL producers (68.9%). The occurrence of ESBL was significantly higher among isolates from inpatients than outpatients [95 (50.5%) vs. 27(32.9%)] (p = 0.008). The occurrence of ESBL was significantly higher among isolates from children than in adults [84 (54.9%) vs. 38(32.5%)] (p < 0.001).</p> <p>Conclusions</p> <p>High prevalence of ESBL-producing <it>E. coli </it>and <it>Klebsiella spp </it>strains was found among inpatients and children. Most of the ESBL- producing isolates were multi-drug resistant making available therapeutic choices limited. We recommend continued antibiotic surveillance as well comprehensive multi-center studies to address the emerging problem of ESBL-associated infections in order to preserve the continued usefulness of most antimicrobial drugs. Further more conducting molecular studies will help to evaluate the various ESBL types.</p

Co-variations of Cholera with Climatic and Environmental Parameters in Coastal Regions of Tanzania

The bacterium causing cholera, Vibrio cholerae, is essentially a marine organism and its ecological dynamics have been linked to oceanographic conditions and climate. We used autoregressive models with external inputs to identify potential relationships between number of cholera cases in the coastal regions of mainland Tanzania with climatic and environmental indices (maximum air temperature, sea surface temperature, wind speed and chlorophyll a). Results show that between 2004 and 2010 coastal regions of mainland Tanzania with approximately 21% of the total population accounted for approximately 50% of the cases and 40% of the total mortality. Significant co-variations were found between seasonally adjusted cases and coastal ocean chlorophyll a and to some degree sea surface temperature, both lagged by one to four months. Cholera cases in Dar es Salaam were also weakly related to the Indian Ocean Dipole Mode Index lagged by 5 months, suggesting that it may be possible to predict Cholera outbreaks for Dar es Salaam 5 months ahead of time. The results also suggest that the severity of cholera in coastal regions is set by conditions in the ocean and that longer-term environmental and climate parameters may be used to predict cholera outbreaks along the coastal regions

Bacteraemia, Malaria, and Case Fatality Among Children Hospitalized With Fever in Dar es Salaam, Tanzania

Background Febrile illness is the commonest cause of hospitalization in children <5 years in sub-Saharan Africa, and bacterial blood stream-infections and malaria are major causes of death. Methods From March 2017 to July 2018, we enrolled 2226 children aged 0-5 years hospitalized due to fever in four major public hospitals of Dar es Salaam namely; Amana, Temeke and Mwananyamala Regional Hospitals and Muhimbili National Hospital. We recorded social demographic and clinical data, performed blood-culture and HIV-antibody testing. We used qPCR to quantify Plasmodium falciparum parasitaemia and Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) to identify bacterial isolates. Disk diffusion method was used for antimicrobial susceptibility testing. Results Nineteen percent of the children (426/2226) had pathogens detected from blood. Eleven percent (236/2226) of the children had bacteraemia/fungaemia and 10% (204/2063) had P. falciparum malaria. Ten children had concomitant malaria and bacteraemia. Gram-negative bacteria (64%) were more frequent than Gram-positive (32%) and fungi (4%). Over fifty percent of Gram-negative bacteria were extended-spectrum beta-lactamase (ESBL) producers and multidrug resistant. Methicillin resistant Staphylococcus aureus (MRSA) was found in 11/42 (26.2%). The most severe form of clinical malaria was associated with high parasitaemia (>four million genomes/µL) of P. falciparaum in plasma. Overall, in-hospital death was 4% (89/2146) and it was higher in children with bacteraemia (8%, 18/227) than malaria (2%, 4/194, P=0.007). Risk factors for death were bacteraemia (p=0.03), unconsciousness at admission (p<0.001) and admission at a tertiary hospital (p=0.003). Conclusions Compared to previous studies in this region, our study showed a reduction in malaria prevalence, a decrease in in-hospital mortality and an increase in antimicrobial resistance (AMR) including ESBLs and multidrug resistance. An increase of AMR highlights the importance of continued strengthening of diagnostic capability and antimicrobial stewardship programs. We also found malaria and bacteraemia contributed equally in causing febrile illness but bacteraemia caused higher in-hospital death. The most severe form of clinical malaria was associated with P. falciparum parasitaemia

Molecular characterisation of the first New Delhi metallo-β-lactamase 1-producing Acinetobacter baumannii from Tanzania

Background We aimed to characterise the genetic determinants and context of two meropenem-resistant clinical isolates of Acinetobacter baumannii isolated from children hospitalised with bloodstream infections in Dar es Salaam, Tanzania. Methods Antimicrobial susceptibility was determined by disc diffusion E-test and broth microdilution. Genomes were completed using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing reads and characterisation of the genetic context of resistance genes, multi-locus sequence types (ST) and phylogenetic analysis were determined bioinformatically. Results Twelve Acinetobacter baumannii were isolated from 2226 blood cultures and two of which were meropenem resistant. The two meropenem resistant isolates, belonging to distinct STs; ST374 and ST239, were found to harbour blaNDM-1, which was chromosomally located in isolate DT0544 and plasmid located in isolate DT01139. The genetic environment of blaNDM- 1 shows the association of insertion sequence ISAba125 with blaNDM-1 in both isolates. Both isolates also harboured genes conferring resistance to other β-lactams, aminoglycosides and cotrimoxazole. Conclusions This is the first report of NDM-1 producing isolates of A. baumannii from Tanzania. The genetic context of the blaNDM-1 provides further evidence of the importance of ISAba125 in 44 the spread of blaNDM-1 in A. baumannii. Local surveillance should be strengthened to keep clinicians updated on the incidence of these and other multidrug-resistant and difficult-to- treat bacteria. Accession numbers: The chromosomal and plasmid sequences of DT0544 and DT01139 were submitted to GenBank with accession numbers PRJNA679703 and PRJNA679704, respectively

Age specific aetiological agents of diarrhoea in hospitalized children aged less than five years in Dar es Salaam, Tanzania

\ud This study aimed to determine the age-specific aetiologic agents of diarrhoea in children aged less than five years. The study also assessed the efficacy of the empiric treatment of childhood diarrhoea using Integrated Management of Childhood Illness (IMCI) guidelines. This study included 280 children aged less than 5 years, admitted with diarrhoea to any of the four major hospitals in Dar es Salaam. Bacterial pathogens were identified using conventional methods. Enzyme Linked Immunosorbent Assay (ELISA) and agglutination assay were used to detect viruses and intestinal protozoa, respectively. Antimicrobial susceptibility was determined using Kirby-Bauer disk diffusion method. At least one of the searched pathogens was detected in 67.1% of the cases, and mixed infections were detected in 20.7% of cases. Overall, bacteria and viruses contributed equally accounting for 33.2% and 32.2% of all the cases, respectively, while parasites were detected in 19.2% patients. Diarrhoeagenic Escherichia coli (DEC) was the most common enteric pathogen, isolated in 22.9% of patients, followed by Cryptosporidium parvum (18.9%), rotavirus (18.1%) and norovirus (13.7%). The main cause of diarrhoea in children aged 0 to 6 months were bacteria, predominantly DEC, while viruses predominated in the 7-12 months age group. Vibrio cholerae was isolated mostly in children above two years. Shigella spp, V. cholerae and DEC showed moderate to high rates of resistance to erythromycin, ampicillin, chloramphenicol and tetracycline (56.2-100%). V. cholerae showed full susceptibility to co-trimoxazole (100%), while DEC and Shigella showed high rate of resistance to co-trimoxazole; 90.6% and 93.3% respectively. None of the bacterial pathogens isolated showed resistance to ciprofloxacin which is not recommended for use in children. Cefotaxime resistance was found only in 4.7% of the DEC. During the dry season, acute watery diarrhoea is the most common type of diarrhoea in children under five years in Dar es Salaam and is predominantly due to DEC, C. parvum, rotaviruses and noroviruses. Constant antibiotic surveillance is warranted as bacteria were highly resistant to various antimicrobial agents including co-trimoxazole and erythromycin which are currently recommended for empiric treatment of diarrhoea.\u

PCR Targeting Plasmodium Mitochondrial Genome of DNA Extracted from Dried Blood on Filter Paper Compared to Whole Blood.

Monitoring mortality and morbidity attributable to malaria is paramount to achieve elimination of malaria. Diagnosis of malaria is challenging and PCR is a reliable method for identifying malaria with high sensitivity. However, blood specimen collection and transport can be challenging and obtaining dried blood spots (DBS) on filter paper by finger-prick may have advantages over collecting whole blood by venepuncture. DBS and whole blood were collected from febrile children admitted at the general paediatric wards at a referral hospital in Dar es Salaam, Tanzania. DNA extracted from whole blood and from DBS was tested with a genus-specific PCR targeting the mitochondrial Plasmodium genome. Positive samples by PCR of DNA from whole blood were tested with species-specific PCR targeting the 18S rRNA locus, or sequencing if species-specific PCR was negative. Rapid diagnostic test (RDT) and thin blood smear microscopy was carried out on all patients where remnant whole blood and a blood slide, respectively, were available. Positivity of PCR was 24.5 (78/319) and 11.2% (52/442) by whole blood and DBS, respectively. All samples positive on DBS were also positive on Plasmodium falciparum species-specific PCR. All RDT positive cases were also positive by DBS PCR. All but three cases with positive blood slides were also positive by DBS. In this study, PCR for malaria mitochondrial DNA extracted from whole blood was more sensitive than from DBS. However, DBS are a practical alternative to whole blood and detected approximately the same number of cases as RDTs and, therefore, remain relevant for research purposes

Identification of diarrheagenic Escherichia coli isolated from infants and children in Dar es Salaam, Tanzania

<p>Abstract</p> <p>Background</p> <p>Relatively few studies have been done in Tanzania to detect and classify diarrheagenic <it>Escherichia coli </it>(DEC) strains among children with diarrhea. This study aimed at investigating DEC among children in Dar es Salaam aged less than five years hospitalized due to acute/persistent diarrhea.</p> <p>Methods</p> <p>DEC were isolated from stool samples collected from two hundred and eighty children with acute/persistent diarrhea at Muhimbili National Hospital and Ilala and Mwananyamala Municipal Hospitals in Dar es Salaam. A multiplex PCR system method was used to detect a species specific gene for <it>E.coli </it>and ten different virulence genes for detection of five pathogroups of DEC namely enteroaggregative- (EAEC), enteropathogenic- (EPEC), enterotoxigenic- (ETEC), enteroinvasive- (EIEC) and enterohemorghagic- <it>Escherichia coli </it>(EHEC).</p> <p>Results</p> <p>Sixty-four patients (22.9%) harbored DEC. Forty-one of them (14.6%) were categorized as EAEC. Most of the EAEC (82.9%) were classified as typical EAEC possessing the <it>aggR </it>gene, and 92.6% carried the <it>aat </it>gene. Isolates from thirteen patients were EPEC (4.6%) and most of these (92.3%) were typical EPEC with both <it>eae </it>and <it>bfpA </it>genes. Ten isolates were identified as ETEC (3.6%) with only the heat stable toxin; either <it>st1a </it>or <it>st1b </it>but not both. Age wise, EAEC and EPEC were significantly more prevalent among the age group 0–6 months (p < 0.05). Genes for EHEC (<it>stx</it>₁and <it>stx</it>₂) and EIEC <it>(ial</it>) were not detected in this study group.</p> <p>Conclusion</p> <p>The results show a high proportion of DEC among Tanzanian children with diarrhea, with typical EAEC and typical EPEC predominating. The use of primers for both variants of ST1 (st1a and st1b) increased the sensitivity for detection of ETEC strains.</p

Prevalence of enteropathogenic viruses and molecular characterization of group A rotavirus among children with diarrhea in Dar es Salaam Tanzania

Different groups of viruses have been shown to be responsible for acute diarrhea among children during their first few years of life. Epidemiological knowledge of viral agents is critical for the development of effective preventive measures, including vaccines. In this study we determined the prevalence of the four major enteropathogenic viruses - rotavirus, norovirus, adenovirus and astrovirus - was determined in 270 stool samples collected from children aged 0 - 60 months who were admitted with diarrhea in four hospitals in Dar es Salaam, Tanzania, using commercially available ELISA kits. In addition, the molecular epidemiology of group A rotavirus was investigated using reverse transcriptase multiplex polymerase chain reaction (RT-PCR). At least one viral agent was detected in 87/270 (32.2%) of the children. The prevalence of rotavirus, norovirus, adenovirus and astrovirus was 18.1%, 13.7%, 2.6% and 0.4%, respectively. In most cases (62.1%) of viruses were detected in children aged 7-12 months. The G and P types (VP7 and VP4 genotypes respectively) were further investigated in 49 rotavirus ELISA positive samples. G9 was the predominant G type (81.6%), followed by G1 (10.2%) and G3 (0.2%). P[8] was the predominant P type (83.7%), followed by P[6] (0.4%) and P[4] (0.2%). The following G and P types were not detected in this study population; G2, G4, G8 G10, P[9], P[10] and P[11]. The dominating G/P combination was G9P[8], accounting for 39 (90.7%) of the 43 fully characterized strains. Three (6.1%) of the 49 rotavirus strains could not be typed. Nearly one third of children with diarrhea admitted to hospitals in Dar es Salaam had one of the four viral agents. The predominance of rotavirus serotype G9 may have implication for rotavirus vaccination in Tanzania

Spatiotemporal variation in risk of Shigella infection in childhood : a global risk mapping and prediction model using individual participant data

BACKGROUND: Diarrhoeal disease is a leading cause of childhood illness and death globally, and Shigella is a major aetiological contributor for which a vaccine might soon be available. The primary objective of this study was to model the spatiotemporal variation in paediatric Shigella infection and map its predicted prevalence across low-income and middle-income countries (LMICs). METHODS: Individual participant data for Shigella positivity in stool samples were sourced from multiple LMIC-based studies of children aged 59 months or younger. Covariates included household-level and participant-level factors ascertained by study investigators and environmental and hydrometeorological variables extracted from various data products at georeferenced child locations. Multivariate models were fitted and prevalence predictions obtained by syndrome and age stratum. FINDINGS: 20 studies from 23 countries (including locations in Central America and South America, sub-Saharan Africa, and south and southeast Asia) contributed 66 563 sample results. Age, symptom status, and study design contributed most to model performance followed by temperature, wind speed, relative humidity, and soil moisture. Probability of Shigella infection exceeded 20% when both precipitation and soil moisture were above average and had a 43% peak in uncomplicated diarrhoea cases at 33°C temperatures, above which it decreased. Compared with unimproved sanitation, improved sanitation decreased the odds of Shigella infection by 19% (odds ratio [OR]=0·81 [95% CI 0·76-0·86]) and open defecation decreased them by 18% (OR=0·82 [0·76-0·88]). INTERPRETATION: The distribution of Shigella is more sensitive to climatological factors, such as temperature, than previously recognised. Conditions in much of sub-Saharan Africa are particularly propitious for Shigella transmission, although hotspots also occur in South America and Central America, the Ganges-Brahmaputra Delta, and the island of New Guinea. These findings can inform prioritisation of populations for future vaccine trials and campaigns. FUNDING: NASA, National Institutes of Health-The National Institute of Allergy and Infectious Diseases, and Bill & Melinda Gates Foundation.publishedVersionPeer reviewe

Bacterial isolates and drug susceptibility patterns of urinary tract infection among pregnant women at Muhimbili National Hospital in Tanzania

Urinary tract infection (UTI) during pregnancy may cause complications such as pyelonephritis, hypertensive disease of pregnancy, anemia, chronic renal failure, premature delivery and fetal mortality. This study aimed to identify the etiologic agents of UTI and to determine the patterns of antimicrobial drug susceptibility among pregnant women at Muhimbili National Hospital in Tanzania. Retrospective analysis of 200 mid-stream urine specimens processed for culture and antimicrobial drug susceptibility testing between January 2007 and December 2009 was carried out. Significant bacteriuria (> 105 colony forming units/mL of urine) was found in 42/200 (21%) specimens. Of the 42 isolates, the most commonly isolated bacteria were Escherichia coli 14 (33.3%), Klebsiella spp 9 (21.4%) coagulase negative Staphylococcus 7 (16.7%), Staphylococcus aureus 6 (14.3%), Proteus species 3 (7.1%) and Enterococcus species 3 (7.1%). Low rate to moderately high rate of antimicrobial drug resistance was observed against first line drugs namely, nitrofurantoin 18.7 % (n=16), co-trimoxazole 38.5 % (n=13) and ampicillin 57.7 % (n=26). Relatively low rate of resistance was seen against second line drugs: ciprofloxacin 13.6 % (n=22) and amikacin 5 % (n=20). High rate of resistance was observed in third generation cephalosporin cefotaxime 31.2 % (n=16). Of the Gram-positive organisms tested against vancomicin and methicilin, resistance was found in 25 % (n=13) and 25 % (n=4), respectively. In conclusion, E coli was found to be the common cause of UTI among the pregnant women. Low to moderately high level of resistance was found in first line drugs while high level of resistance was found in third generation cephalosporin. It is recommended to monitor the levels of resistance for nitrofurantoin, fluoroquinolone and cefotaxime and to screen for Extended Spectrum Beta Lactamase production among cefotaxime resistant E. coli and Klebsiella spp