Pediatric HIV care and treatment services in Tanzania: implications for survival.

BACKGROUND: Improving child survival for HIV-infected children remains an important health agenda. We present progress regarding care and treatment services to HIV infected children in Tanzania. METHODS: The National AIDS Control Programme Care and Treatment (CTC 2) database was used to obtain information of all children aged 0-14yearsenrolled in the HIV Care and Treatment Program between January 2011 and December 2014. We assessed eligibility for ART, time from enrolment to ART initiation, nutritional status, and mortality using Kaplan-Meier methods. RESULTS: A total of 29,531 (14,304 boys and 15,227 girls) ART-naive children aged 0-14 years were enrolled during the period, approximately 6700 to 8000 children per year. The male to female ratio was 48:50. At enrolment 72% were eligible for ART, 2-3% of children were positive for TB, and 2-4% were severely malnourished. Between 2011 and 2014, 2368 (8%) died, 9243 (31%) were Lost to Follow-up and 17,920 (61%) were on care or ART. The probability of death was 31% (95% CI 26-35), 43% (40-47), 52% (49-55) and 61% (58-64) by 1,2, 5 and 10 years of age, respectively. The hazard of death was greatest at very young ages (<2 years old), and decreased sharply by 4 years old. Children who were on ART had around 10-15% higher survival over time. CONCLUSIONS: Significant progress has been made regarding provision of paediatric HIV care and treatment in Tanzania. On average 7000 children are enrolled annually, and that approximately two thirds of children diagnosed under the age of 2 years were initiated on ART within a month. Provision of ART as soon as the child is diagnosed is the biggest factor in improving survival. However we noted that i) most children had advanced disease at the time of enrolment ii) approximately two-thirds of children were missing a baseline CD4 measurement and only 35% of children had either a CD4 count or percentage recorded, indicating limited access to CD4 testing services, and iii) 31% were lost to follow-up (LTFU). These challenges need to be addressed to improve early detection, enrolment and retention of HIV-infected children into care and improve documentation of services offered

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

Prevalence and incidence rate of tuberculosis among HIV-infected patients enrolled in HIV care, treatment, and support program in mainland Tanzania.

BACKGROUND: Despite improvements in access to antiretroviral therapy (ART), mortality in people living with human immunodeficiency virus (PLHIV) is still high and primarily attributed to tuberculosis (TB) infection. In Sub-Saharan Africa, approximately 80% of HIV-related mortality cases are associated with TB. Relatively little is known about the incidence of TB among PLHIV in Tanzania and the determinant factors. We report the prevalence and incidence rate of confirmed TB and determine association with selected demographic and program-related factors based on data in the national HIV care and treatment program from 2011 to 2014. METHODS: We used the Tanzania National AIDS Control Programme database to obtain information on all HIV clients enrolled in the HIV care and treatment program between January 2011 and December 2014. We analyzed retrospective cohort data to assess the prevalence and TB incidence rate per 1000 person-years. A multivariable Cox proportional hazards regression model was used to estimate hazard ratios and 95% confidence intervals for putatively associated factors. RESULTS: Over 4 years, there were 22,071 confirmed cases of pulmonary TB in 1,323,600 person-years. The overall TB incidence was around 16.7 (95% CI 16.4-16.9) cases per 1000 person-years. The annual incidence rate decreased by 12.4 % from 17.0 (95% CI 16.5-17.4) in 2011 to 14.9 (95% CI 14.5-15.4) in 2014. The TB incidence rate was higher in persons not using ART and in males than in females. The incidence of TB was higher in patients with advanced HIV disease and decreased with increasing age. The overall prevalence of TB was 2.2%, with a peak prevalence of 2.5% in 2013 and was higher among children < 15 years (3.2%) in the same year. CONCLUSION: The study found an overall decrease in the incidence of TB in PLHIV. Our results emphasize the need for early initiation of ART and the provision of TB preventive therapy for those PLHIV without active TB after intensified TB case-finding

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

Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania

Abstract Background Limited information regarding the clonality of circulating E. coli strains in tertiary care hospitals in low and middle-income countries is available. The purpose of this study was to determine the serotypes, antimicrobial resistance and virulence genes. Further, we carried out a phylogenetic tree reconstruction to determine relatedness of E. coli isolated from patients in a tertiary care hospital in Tanzania. Methods E. coli isolates from inpatients admitted at Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced at KCMC hospital. Sequence analysis was done for identification of resistance genes, Multi-Locus Sequence Typing, serotyping, and virulence genes. Phylogeny reconstruction using CSI Phylogeny was done to ascertain E. coli relatedness. Stata 13 (College Station, Texas 77,845 USA) was used to determine Cohen’s kappa coefficient of agreement between the phenotypically tested and whole genome sequence predicted antimicrobial resistance. Results Out of 38 E. coli isolates, 21 different sequence types (ST) were observed. Eight (21.1%) isolates belonged to ST131; of which 7 (87.5.%) were serotype O25:H4. Ten (18.4%) isolates belonged to ST10 clonal complex; of these, four (40.0%) were ST617 with serotype O89:H10. Twenty-eight (73.7%) isolates carried genes encoding beta-lactam resistance enzymes. On average, agreement across all drugs tested was 83.9%. Trimethoprim/sulphamethoxazole (co-trimoxazole) showed moderate agreement: 45.8%, kappa =15% and p = 0.08. Amoxicillin-clavulanate showed strongest agreement: 87.5%, kappa = 74% and p = 0.0001. Twenty-two (57.9%) isolates carried virulence factors for host cells adherence and 25 (65.7%) for factors that promote E. coli immune evasion by increasing survival in serum. The phylogeny analysis showed that ST131 clustering close together whereas ST10 clonal complex had a very clear segregation of the ST617 and a mix of the rest STs. Conclusion There is a high diversity of E. coli isolated from patients admitted to a tertiary care hospital in Tanzania. This underscores the necessity to routinely screen all bacterial isolates of clinical importance in tertiary health care facilities. WGS use for laboratory-based surveillance can be an effective early warning system for emerging pathogens and resistance mechanisms in LMICs

Detection of CTX-M-15 beta-lactamases in Enterobacteriaceae causing hospital- and community-acquired urinary tract infections as early as 2004, in Dar es Salaam, Tanzania

Abstract Background The spread of Extended Spectrum β-lactamases (ESBLs) among Enterobacteriaceae and other Gram-Negative pathogens in the community and hospitals represents a major challenge to combat infections. We conducted a study to assess the prevalence and genetic makeup of ESBL-type resistance in bacterial isolates causing community- and hospital-acquired urinary tract infections. Methods A total of 172 isolates of Enterobacteriaceae were collected in Dar es Salaam, Tanzania, from patients who met criteria of community and hospital-acquired urinary tract infections. We used E-test ESBL strips to test for ESBL-phenotype and PCR and sequencing for detection of ESBL genes. Results Overall 23.8% (41/172) of all isolates were ESBL-producers. ESBL-producers were more frequently isolated from hospital-acquired infections (32%, 27/84 than from community-acquired infections (16%, 14/88, p < 0.05). ESBL-producers showed high rate of resistance to ciprofloxacin (85.5%), doxycycline (90.2%), gentamicin (80.5%), nalidixic acid (84.5%), and trimethoprim-sulfamethoxazole (85.4%). Furthermore, 95% of ESBL-producers were multi-drug resistant compared to 69% of non-ESBL-producers (p < 0.05). The distribution of ESBL genes were as follows: 29/32 (90.6%) bla CTX-M-15, two bla SHV-12, and one had both bla CTX-M-15 and bla SHV-12. Of 29 isolates carrying bla CTX-M-15, 69% (20/29) and 31% (9/29) were hospital and community, respectively. Bla SHV-12 genotypes were only detected in hospital-acquired infections. Conclusion bla CTX-M-15 is a predominant gene conferring ESBL-production in Enterobacteriaceae causing both hospital- and community-acquired infections in Tanzania