Polymicrobial bloodstream infections a risk factor for mortality in neonates at the national hospital, Tanzania: A case-control study.

BACKGROUND: Polymicrobial bloodstream infections (BSI) are difficult to treat since empiric antibiotics treatment are frequently less effective against multiple pathogens. The study aimed to compare outcomes in patients with polymicrobial and monomicrobial BSIs. METHODS: The study was a retrospective case-control design conducted at Muhimbili National Hospital for data processed between July 2021 and June 2022. Cases were patients with polymicrobial BSI, and controls had monomicrobial BSI. Each case was matched to three controls by age, admitting ward, and duration of admission. Logistic regression was performed to determine independent risk factors for in-hospital and 30-day mortality. RESULTS: Fifty patients with polymicrobial BSI and 150 with monomicrobial BSI were compared: the two arms had no significant differences in sex and comorbidities. The most frequent bacteria in polymicrobial BSI were Klebsiella pneumoniae 17% (17/100) and Enterobacter species 15% (15/100). In monomicrobial BSI, S. aureus 17.33% (26/150), Klebsiella pneumoniae 16.67% (25/150), and Acinetobacter species 15% (15/150) were more prevalent. Overall, isolates were frequently resistant to multiple antibiotics tested, and 52% (130/250) were multidrug resistance. The 30-day and in-hospital mortality were 33.5% (67/200) and 36% (72/200), respectively. On multivariable analysis, polymicrobial BSIs were independent risk factors for both in-hospital mortality (aOR 2.37, 95%CI 1.20-4.69, p = 0.01) and 30-day mortality (aOR 2.05, 95%CI 1.03-4.08), p = 0.04). In sub-analyses involving only neonates, polymicrobial BSI was an independent risk factor for both 30-day mortality (aOR 3.13, 95%CI 1.07-9.10, p = 0.04) and in-hospital mortality (aOR 5.08, 95%CI 1.60-16.14, p = 0.006). Overall, the median length of hospital stay post-BSIs was numerically longer in patients with polymicrobial BSIs. CONCLUSION: Overall, polymicrobial BSI was a significant risk for mortality. Patients with polymicrobial BSI stay longer at the hospital than those with monomicrobial BSI. These findings call for clinicians to be more aggressive in managing polymicrobial BSI.

Predominance of multidrug-resistant Salmonella Typhi genotype 4.3.1 with low-level ciprofloxacin resistance in Zanzibar.

BACKGROUND: Typhoid fever is a common cause of febrile illness in low- and middle-income countries. While multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) has spread globally, fluoroquinolone resistance has mainly affected Asia. METHODS: Consecutively, 1038 blood cultures were obtained from patients of all age groups with fever and/or suspicion of serious systemic infection admitted at Mnazi Mmoja Hospital, Zanzibar in 2015-2016. S. Typhi were analyzed with antimicrobial susceptibility testing and with short read (61 strains) and long read (9 strains) whole genome sequencing, including three S. Typhi strains isolated in a pilot study 2012-2013. RESULTS: Sixty-three S. Typhi isolates (98%) were MDR carrying blaTEM-1B, sul1 and sul2, dfrA7 and catA1 genes. Low-level ciprofloxacin resistance was detected in 69% (43/62), with a single gyrase mutation gyrA-D87G in 41 strains, and a single gyrA-S83F mutation in the non-MDR strain. All isolates were susceptible to ceftriaxone and azithromycin. All MDR isolates belonged to genotype 4.3.1 lineage I (4.3.1.1), with the antimicrobial resistance determinants located on a composite transposon integrated into the chromosome. Phylogenetically, the MDR subgroup with ciprofloxacin resistance clusters together with two external isolates. CONCLUSIONS: We report a high rate of MDR and low-level ciprofloxacin resistant S. Typhi circulating in Zanzibar, belonging to genotype 4.3.1.1, which is widespread in Southeast Asia and African countries and associated with low-level ciprofloxacin resistance. Few therapeutic options are available for treatment of typhoid fever in the study setting. Surveillance of the prevalence, spread and antimicrobial susceptibility of S. Typhi can guide treatment and control efforts.

Antibiotic use at a tertiary hospital in Tanzania: findings from a point prevalence survey.

BACKGROUND: In Tanzania, data on antibiotic use at the patient level is scarce, and intervention measures to optimize antibiotic use and reduce antimicrobial resistance are rarely performed. OBJECTIVES: To describe antibiotic use at Muhimbili National Hospital. METHODS: This was a point prevalence survey on antibiotic use conducted at Muhimbili National Hospital in August-September 2022. The World Health Organization point prevalence survey data collection tool was used to collect patients' information from the files. All patients admitted to the wards on the day of the survey were included. RESULTS: Overall, 47% (185/397) of admitted patients were on at least one antibiotic during the survey. All antibiotics prescribed were for empirical treatment and guideline compliance was low, at 45%. Of 185 patients who received antibiotics, the most common indication was community acquired infection (55%) and 36% had no documentation of the reasons for prescribing antibiotics. Almost 75% of the antibiotics were administered parenterally, with only 2% switching to oral route. Microbiological tests were performed in only 9 (5%) patients out of 185 and results were available for only one patient. Of all participants, 52% received two or more antibiotic in combination, with the combination ceftriaxone-metronidazole being most frequently prescribed, followed by the combination of ampicillin, cloxacillin, and gentamicin. For individual antibiotics, ceftriaxone was the most frequently prescribed antibiotic accounting for 28% (79/283), followed by metronidazole (24%) and amoxicillin-clavulanic acid (11%). CONCLUSION: The findings of a high prevalence of antibiotic use, inadequate use of bacterial culture, and frequent empiric antibiotic treatment suggests the need for strengthening diagnostic and antimicrobial stewardship programs. Furthermore, this study has identified areas for quality improvement, including education programs focusing on prescription practice.

Aetiology of ear infection and antimicrobial susceptibility pattern among patients attending otorhinolaryngology clinic at a tertiary hospital in Dar es Salaam, Tanzania: a hospital-based cross-sectional study.

OBJECTIVES: To determine the aetiological pathogens causing ear infections and their antimicrobial susceptibility patterns among patients with ear complaints at a tertiary hospital in Dar es Salaam. DESIGN: Hospital-based cross-sectional study. SETTINGS: Otorhinolaryngology clinic at Muhimbili National Hospital, Dar es Salaam, Tanzania. PARTICIPANTS: Patients presenting with signs and symptoms of ear infection. MAIN OUTCOME MEASURE: Bacteria and fungi isolated from ear swab specimens of patients presenting with signs and symptoms of ear infection; and antimicrobial susceptibility patterns of isolated bacteria. RESULTS: Two hundred and fifty-five participants were enrolled, with a median age of 31 years and an IQR of 15-49. Otitis externa was the predominant type of ear infection, accounting for 45.1%. We observed positive bacteria culture in 53.3% of study participants, in which 41% of isolates were obtained from patients with chronic suppurative otitis media. Moreover, Staphylococcus aureus (27.3%) and Pseudomonas aeruginosa (24.2%) were the most frequently isolated bacteria, while Candida spp, 12 (63.8%) and Aspergillus spp, 9 (36.2%) were the only isolated fungi. Furthermore, we report that 93% of isolated Enterobacterales were resistant to amoxicillin/clavulanic acid, and 73% were resistant to ceftazidime. In addition, we detected 34.4% extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and 44.4% methicillin-resistance S. aureus (MRSA). We also found that 22% of the bacteria isolates were resistant to ciprofloxacin, a primary topical antibiotic used in managing ear infections. CONCLUSIONS: The findings from this study reveal that the leading aetiological agent of ear infection is bacteria. Furthermore, our findings show a significant proportion of ESBL-PE and MRSA-causing ear infections. Hence, detecting multidrug-resistant bacteria is crucial to improving ear infection management.

Predominance of non-Candida albicans species oral colonisation among patients on anticancer therapy: findings from a cross-sectional study in Tanzania.

OBJECTIVES: This study aimed to determine the oral carriage prevalence of Candida species and identify factors associated with the carriage of Candida species among patients with cancer on treatment. DESIGN: A hospital-based cross-sectional study. SETTING: The study was conducted at a tertiary-level cancer hospital Ocean Road Cancer Institute (ORCI), Dar es Salaam, Tanzania. PARTICIPANTS: We enrolled 196 participants who consented to join the study. Oral swabs were collected from all participants and inoculated onto Sabouraud dextrose agar supplemented with 50 mg/mL gentamicin and 50 mg/mL chloramphenicol, and chromogenic agar for phenotypic identification of Candida species. PRIMARY OUTCOME: The study reported the high prevalence of oral carriage of Candida species among patients with cancer on treatment at the tertiary-level cancer hospital in Dar es Salaam, Tanzania. RESULTS: A total of 196 participants were enrolled in the study. The overall oral carriage of Candida species was 37.8% (74/196). The prevalence was higher among patients undergoing chemotherapy and radiotherapy (44.4%) than those in monotherapy (13.3% chemotherapy, 20% radiotherapy). Candida krusei was the most common isolated species, 48.6% (36/74). Head and neck (adjusted OR (aOR) 15.09, 95% CI 3.05 to 74.59, p=0.00), gastrointestinal (aOR 14.14, 95% CI 2.25 to 88.63, p=0.00) malignancies and diabetes (aOR 3.18, 95% CI 1.03 to 9.77, p=0.04) were factors independently associated with oral carriage of Candida species. CONCLUSION: The oral carriage of Candida species among patients with cancer receiving treatment at ORCI is high, mainly due to C. krusei species. This is alarming since C. krusei has intrinsic resistance to fluconazole, a common antifungal agent used to manage adult fungal infections. Therefore, efforts should be put into conducting regular check-ups for such opportunistic pathogens as they can lead to subsequent infections. Furthermore, studies conducted to determine the antifungal profile of the causative agents are warranted since different causative agents might have different profiles.

Fluoroquinolone resistance among fecal extended spectrum ßeta lactamases positive Enterobacterales isolates from children in Dar es Salaam, Tanzania.

BACKGROUND: Fluoroquinolones have been, and continue to be, routinely used for treatment of many bacterial infections. In recent years, most parts of the world have reported an increasing trend of fluoroquinolone resistant (FQR) Gram-negative bacteria. METHODS: A cross-sectional study was conducted between March 2017 and July 2018 among children admitted due to fever to referral hospitals in Dar es Salaam, Tanzania. Rectal swabs were used to screen for carriage of extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-PE). ESBL-PE isolates were tested for quinolone resistance by disk diffusion method. Randomly selected fluroquinolone resistant isolates were characterized by using whole genome sequencing. RESULTS: A total of 142 ESBL-PE archived isolates were tested for fluoroquinolone resistance. Overall phenotypic resistance to ciprofloxacin, levofloxacin and moxifloxacin was found in 68% (97/142). The highest resistance rate was seen among Citrobacter spp. (100%, 5/5), followed by Klebsiella. pneumoniae (76.1%; 35/46), Escherichia coli (65.6%; 42/64) and Enterobacter spp. (31.9%; 15/47). Whole genome sequencing (WGS) was performed on 42 fluoroquinolone resistant-ESBL producing isolates and revealed that 38/42; or 90.5%, of the isolates carried one or more plasmid mediated quinolone resistance (PMQR) genes. The most frequent PMQR genes were aac(6')-lb-cr (74%; 31/42), followed by qnrB1 (40%; 17/42), oqx, qnrB6 and qnS1. Chromosomal mutations in gyrA, parC and parE were detected among 19/42 isolates, and all were in E. coli. Most of the E. coli isolates (17/20) had high MIC values of > 32 µg/ml for fluoroquinolones. In these strains, multiple chromosomal mutations were detected, and all except three strains had additional PMQR genes. Sequence types, ST131 and ST617 predominated among E. coli isolates, while ST607 was more common out of 12 sequence types detected among the K. pneumoniae. Fluoroquinolone resistance genes were mostly associated with the IncF plasmids. CONCLUSION: The ESBL-PE isolates showed high rates of phenotypic resistance towards fluoroquinolones likely mediated by both chromosomal mutations and PMQR genes. Chromosomal mutations with or without the presence of PMQR were associated with high MIC values in these bacteria strains. We also found a diversity of PMQR genes, sequence types, virulence genes, and plasmid located antimicrobial resistance (AMR) genes towards other antimicrobial agents.

Predominance of Multidrug-Resistant Gram-Negative Bacteria on Contaminated Surfaces at a Tertiary Hospital in Tanzania: A Call to Strengthening Environmental Infection Prevention and Control Measures.

The spreading of multidrug resistance (MDR) strains in the hospital settings via contaminated surfaces have been increasingly reported where Gram-negative bacteria have been implicated in causing most nosocomial infections. This study aimed to determine the rate of contamination with multi-resistant gram-negative bacteria in the hospital environment. A cross-sectional study was conducted at Muhimbili National Hospital paediatric department, between July and August 2020. Non-repetitive surface swab samples were collected from predefined surfaces and medical device surfaces, and cultured on MacConkey agar with and without antibiotics. Isolates were identified using biochemical test and tested for antibiotic susceptibility using the Kirby-Bauer disk diffusion method. The rate of hospital contamination with Gram-negative bacteria across the Pediatrics units was 30%, with a high rate observed in oncology units (34.8%) and the malnutrition/diarrhoea ward (32.1%). Sink/washing basin had the highest frequency of bacterial contamination (74.2%). We observed a high rate of ESBL (32.5%), with Acinetobacter baumannii, Klebsiella pneumoniae, and E. coli being the predominant ESBL-producing Gram-negative bacteria, while carbapenemase-producing Gram-negative bacteria was detected at 22.8%. Highest resistance rates (63-100%) were observed against ceftriaxone and trimethoprim-sulfamethoxazole. Up to 51% of the Gram-negative bacteria showed resistant to meropenem. MDR strains were detected in 61.4% of Gram-negative bacteria isolated. In conclusion, we observed a high rate of MDR bacteria contaminating hospital surfaces. The higher rate of MDR calls for a need to strengthen infectious prevention control measures, including cleaning practices in the hospital environment, to reduce the risk of transmission of resistant strains to patients and healthcare workers.

Genetic determinants of macrolide and tetracycline resistance in penicillin non-susceptible Streptococcus pneumoniae isolates from people living with HIV in Dar es Salaam, Tanzania.

BACKGROUND: Over one million yearly deaths are attributable to Streptococcus pneumoniae and people living with HIV are particularly vulnerable. Emerging penicillin non-susceptible Streptococcus pneumoniae (PNSP) challenges therapy of pneumococcal disease. The aim of this study was to determine the mechanisms of antibiotic resistance among PNSP isolates by next generation sequencing. METHODS: We assessed 26 PNSP isolates obtained from the nasopharynx from 537 healthy human immunodeficiency virus (HIV) infected adults in Dar es Salaam, Tanzania, participating in the randomized clinical trial CoTrimResist (ClinicalTrials.gov identifier: NCT03087890, registered on 23rd March, 2017). Next generation whole genome sequencing on the Illumina platform was used to identify mechanisms of resistance to antibiotics among PNSP. RESULTS: Fifty percent (13/26) of PNSP were resistant to erythromycin, of these 54% (7/13) and 46% (6/13) had MLSB phenotype and M phenotype respectively. All erythromycin resistant PNSP carried macrolide resistance genes; six isolates had mef(A)-msr(D), five isolates had both erm(B) and mef(A)-msr(D) while two isolates carried erm(B) alone. Isolates harboring the erm(B) gene had increased MIC (> 256 µg/mL) towards macrolides, compared to isolates without erm(B) gene (MIC 4-12 µg/mL) p < 0.001. Using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines, the prevalence of azithromycin resistance was overestimated compared to genetic correlates. Tetracycline resistance was detected in 13/26 (50%) of PNSP and all the 13 isolates harbored the tet(M) gene. All isolates carrying the tet(M) gene and 11/13 isolates with macrolide resistance genes were associated with the mobile genetic element Tn6009 transposon family. Of 26 PNSP isolates, serotype 3 was the most common (6/26), and sequence type ST271 accounted for 15% (4/26). Serotypes 3 and 19 displayed high-level macrolide resistance and frequently carried both macrolide and tetracycline resistance genes. CONCLUSION: The erm(B) and mef(A)-msr(D) were common genes conferring resistance to MLSB in PNSP. Resistance to tetracycline was conferred by the tet(M) gene. Resistance genes were associated with the Tn6009 transposon.

Predictors of Surgical Site Infections among Patients Undergoing Open Urological Surgery at a Tertiary Hospital, Tanzania: A Cross Sectional Study.

Background: Surgical Site Infection (SSI) is one of the major hospital acquired infections, highly associated with prolonged hospitalisation, morbidity and mortality. In open urological surgeries, little is known on magnitude and factors associated with development of SSI. Methods and Materials: The intervention was a cross-sectional prospective observational study performed between August 2015 and March 2016 at Muhimbili National hospital (MNH), Dar es Salaam, Tanzania. Patients who underwent open urological surgery at MNH during the study period and met inclusion criteria were consecutively enrolled, and followed up for 30 days. Patients' and operative characteristics were recorded using standard structured questionnaires. Wound/pus swabs were collected from patients with clinical evidence of SSI for bacteriological processing. Data analysis was performed using SPSS version 20. Results: Of 182 patients who underwent open urological surgery, 22% (40/182) developed SSI. Pre-operative urinary tract infection (aOR 9.73, 95%CI 3.93-24.09, p<.001) and contaminated wound class (aOR 24.997, 95%CI 2.58-242.42, p = .005) were independent predictors for development of SSI. Shaving within 30 hrs before surgical procedure was found to be protective for developing SSI (aOR 0.26, 95%CI 0.09-0.79, p=.02). Escherichia coli (20/40) was the most predominant pathogen in SSI followed by Klebsiella pneumoniae (7/40) and S. aureus (6/40). Gram-negative bacteria were highly resistant to ceftriaxone, gentamicin, amoxicillin-clavulanic acid and trimethoprimsulfamethoxazole. Conclusion: Surgical Site Infection was high in open urological interventions. Pre-operative urinary tract infection and contaminated wound class predicted SSI. Bacteria causing SSI were highly resistant to commonly used antibiotics.

Infective endocarditis in developing countries: An update.

Introduction: Despite advances in diagnostic and treatment, morbidity and mortality due to infective endocarditis (IE) has not decreased. There is a discrepancy in epidemiology of IE between developed and developing countries. Over the last years, increased early detection and consequently prevalence of rheumatic heart disease (RHD) and congenital heart disease (CHD) which are considered predisposing conditions for IE, is noted. Here, we present a review of literature on IE in developing countries. Methods: We conducted a systematic literature search of IE studies in developing countries through PubMed and Embase. We have divided the studies into two groups: studies published before 2015 (group 1) and studies ≥ 2015 (group 2). The outcome was defined as a difference in epidemiology, microbiology, treatment, and mortality over time. The Scale for Assessment of Narrative Review Articles guidelines was applied. Findings: In total, 16 studies were included. The total number of IE cases was 1,098 and 1,505 in groups 1 and 2, respectively. We compared 4/7 cohorts from group 1 (n = 789) with 5/9 cohorts from group 2 (n = 636). Six studies were not included in the comparison because they were interacting between the two cohorts. Males predominated in all studies. Rheumatic heart disease was higher in group 1 than in group 2 (42.3% vs. 30.3%, p < 0.001) while for CHD there was no change (17.6% vs. 16.7%, p = 0.672). Streptococci infections was lower in group 1 than group 2 (26.2% vs. 37.7%, p < 0.001). The proportion of Staphylococcus aureus was 15.3% in group 1 and 23.6% in group 2, p < 0.001. Negative blood culture (NBC) was higher in group 1 than in group 2 (42.2% vs. 34.1%, p = 0.002). Patients in group 1 received more surgery than in group 2 (38.8% vs. 28.8%, p < 0.001). Mortality was similar in the two groups (20.9% vs. 22.3%, p = 0.518). Conclusion: This review shows a scarcity of studies on IE in developing countries. Rheumatic heart disease and congenital heart disease are common predisposing conditions. Other risk factors are prosthetic valves, degenerative valve disease (DVD), intravenous drug use, and human immunodeficiency virus infection. While the proportion of IE cases caused by Streptococcus and Staphylococcus has increased, the number of NBC and patients getting surgery has decreased. Mortality has not changed over time. Timely diagnosis and management of patients with RHD and CHD and comprehensive management of IE are warranted.

Gastrointestinal colonization of extended-spectrum beta-lactamase-producing bacteria among children below five years of age hospitalized with fever in Dar es Salaam, Tanzania.

OBJECTIVES: Gastrointestinal colonization of extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) is of concern because prior colonization increases risk for subsequent infections. To date, the link between ESBL-PE faecal carriage and the risk of subsequent ESBL-PE infection has not been well established, and information on carriage of such pathogens among children with invasive infections such as bloodstream infections (BSI) remains to be explored worldwide. METHODS: This cross-sectional study was conducted among children under the age of 5 years admitted for febrile illness in Dar es Salaam, Tanzania, between March 2017 and July 2018. We used rectal swabs to screen for ESBL-PE using selective media, ChromID ESBL. Bacterial isolates were identified by MALDI-TOF. Blood cultures were drawn from all children. Antimicrobial susceptibility testing was done using a disk diffusion method. ESBL alleles were identified by real-time PCR and sequencing. RESULTS: The overall prevalence of ESBL-PE carriage was 56% (112/200) and was highest among children 4 to 6 months old (17/21, 81%) (P = 0.05). Children with BSI had high ESBL-PE carriage (78.4%) compared to those without BSI (53.1%) (P = 0.02; aOR 3.4, 95% confidence interval 1.20-9.58). The most common isolate was E. coli (64/112, 45%). Sixteen pairs of ESBL-PE isolates (from the gut and from blood) had a similar antimicrobial susceptibility profile. We detected blaCTX-M gene in 97% of all phenotypically detected ESBL-PE; among those, blaCTX-M-15 was dominant (99%). CONCLUSION: We report a high prevalence of ESBL-PE faecal carriage among children with BSI in Tanzania. Colonization of ESBL-PE was a risk factor for ESBL-BSI.

Colonization of Extended-spectrum ß-lactamase producing Enterobacterales and meticillin-resistant S. aureus in the intensive care unit at a tertiary hospital in Tanzania: Implications for Infection control and prevention.

Background: Multi-drug resistant (MDR) bacteria pose a major global threat to public-health and are of particular concern to hospitalized intensive care unit (ICU) patients. This study aimed at addressing the burden of MDR and the associated factors at admission to ICU. Methods: This was a cross-sectional study conducted at the ICU of a tertiary hospital in Tanzania. Rectal and anterior nares swabs were collected within 48 hours of ICU admission to screen for extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and meticillin-resistant Staphylococcus aureus (MRSA), respectively. Results: The proportion of fecal carriage for ESBL-PE at admission to ICU was 54.54% (95% CI, 47.52-61.39), and nasal carriage for MRSA was 9.32% (95%CI, 5.67-14.93). The nasal MRSA colonization (OR = 1.52) and fecal carriage for ESBL-PE (OR=1.38) were more likely in participants who had received antibiotics before ICU admission than not, but association was not statistically significant. Hospitalization for ≥2 days (OR=1.18) was associated with fecal carriage of ESBL-PE, though not statistically significant. Overall, 66% and 73.5% of patients received antibiotics before and upon admission to ICU, respectively. Ceftriaxone, metronidazole and meropenem were commonly prescribed antibiotics. More than 84% of Enterobacterales were resistant to ciprofloxacin and trimethoprim-sulfamethoxazole, and 2.90% were resistant to meropenem. MRSA isolates showed a high rate of resistance to gentamicin and erythromycin. Conclusion: MDR bacteria are common in patients admitted to ICU. To reduce the risk associated with MDR, we recommend use of simple screening methods to screen for MDR at ICU admission as part of infection control and prevention.

First identification of bla NDM-5 producing Escherichia coli from neonates and a HIV infected adult in Tanzania.

Introduction. Carbapenem-resistant members of the family Enterobacteriaceae are emerging as a global public-health threat and cause substantial challenges in clinical practice.Gap Statement. There is a need for increased and continued genomic surveillance of antimicrobial resistance genes globally in order to detect outbreaks and dissemination of clinically important resistance genes and their associated mobile genetic elements in human pathogens.Aim. To describe the resistance mechanisms of carbapenem-resistant Escherichia coli.Methods. Rectal swabs from neonates and newly diagnosed human immunodeficiency virus (HIV) infected adults were collected between April 2017 and May 2018 and screened for faecal carriage of carbapenamases and OXA-48 producing members of the family Enterobacteriaceae. Bacterial isolates were identified using matrix assisted laser desorption ionization time of flight mass spectrometry. Antimicrobial susceptibility testing was performed by E-test. Whole genomes of carbapenem-resistant E. coli were investigated using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing reads.Results. Three carbapenem-resistant E. coli were detected, two from neonates and one from an HIV infected adult. All three isolates carried bla NDM-5. Two E. coli from neonates belonged to ST167 and bla NDM-5 co-existed with bla CTX-M-15 and bla OXA-01, and all were carried on IncFIA type plasmids. The E. coli from the HIV infected adult belonged to ST2083, and carried bla NDM-5 on an IncX3 type plasmid and bla CMY-42 on an IncI type plasmid. All bla NDM-5 carrying plasmids contained conjugation related genes. In addition, E. coli from the HIV infected adult carried three more plasmid types; IncFIA, IncFIB and Col(BS512). One E. coli from a neonate also carried one extra plasmid Col(BS512). All three E. coli harboured resistance genes to fluoroquinolone, aminoglycosides, sulfamethoxazole, trimethoprim, macrolides and tetracycline, carried on the IncFIA type plasmid. Furthermore, E. coli from the neonates carried a chloramphenicol resistance gene (catB3), also on the IncFIA plasmid. All three isolates were susceptible to colistin.Conclusion. This is the first report, to our knowledge, from Tanzania detecting bla NDM-5 producing E. coli. The carbapenemase gene was carried on an IncFIA and IncX3 type plasmids. Our findings highlight the urgent need for a robust antimicrobial resistance (AMR) surveillance system to monitor and rapidly report on the incidence and spread of emerging resistant bacteria in Tanzania.

Seroprevalence and risk factors of Toxoplasmosis among HIV infected women of child-bearing age attending care and treatment clinics in Dar es Salaam, Tanzania.

Background: Toxoplasmosis in HIV-infected women of child-bearing age (HIV-WCB) increases the risk for congenital toxoplasmosis, leading to many complications. However, its magnitude is unknown in this population. Objectives: The study aimed to determine the prevalence and factors associated with toxoplasmosis among HIV-WCB. Methods: This was a cross-sectional study conducted from July to August 2020 among HIV- WCB attending care and treatment clinic (CTC) at Muhimbili National Hospital and Mnazi Mmoja hospital. Questionnaire and TORCH rapid test were used to obtain data and serological testing respectively. Data analysis was done using statistical package for social sciences (SPSS) version 20. Results: Overall, 29.7% of the study participants were positive for anti-T. gondii IgG, whereas none tested positive for IgM. Multivariate analysis showed that the probability of being infected with T. gondii increased by 57.1% for participants who consumed raw vegetables (p=0.005, aOR=0.43, 95%CI = 1.24-8.77). Other common risk factors such as undercooked meat consumption, source of drinking water, and cat ownership at home showed no association. Conclusion: A high number of HIV-WCB have not developed immunity to T. gondii in the study area. Introduction of routine screening during antenatal visits for pregnant women and further epidemiological studies are warranted in the country.

High Level of Multidrug-Resistant Gram-Negative Pathogens Causing Burn Wound Infections in Hospitalized Children in Dar es Salaam, Tanzania.

BACKGROUND: Bacterial infection remains the most common cause of morbidity and mortality in pediatric patients with burn wounds. The increase in infection and multidrug-resistant (MDR) pathogens necessitates a periodic review of antimicrobial susceptibility patterns in the burn units. The study aimed to determine the magnitude of multidrug-resistant Gram-negative (MDRGN) bacteria in children with burn wound infections and describe the resistance patterns in the tertiary and regional hospitals in Dar es Salaam, Tanzania. MATERIALS AND METHODS: The study was a hospital-based cross-sectional study design conducted between May 2017 and February 2018. Bacterial isolates from 103 wound swabs of pediatric patients with burn wounds were identified using conventional methods and API 20E. The antimicrobial susceptibility pattern was determined by the Kirby-Bauer disc diffusion method. Data were analyzed using Statistical Package for Social Science (SPSS) version 23.0. RESULTS: A total of 136 pathogenic Gram-negative organisms were isolated from burn wound infections in pediatric patients. The most isolated Gram-negative bacterium was Pseudomonas aeruginosa (39.0%), followed by Acinetobacter spp. (28.7%) and Klebsiella spp. (16.2%). MDRGN strains made up 80.1% of all Gram-negative isolates. All (100%) Klebsiella spp. and E. coli were MDR, while 69.2% and 79.2% of Acinetobacter spp. and P. aeruginosa, respectively, displayed MDR strains. We observed high levels of resistance to commonly prescribed antibiotics. Among P. aeruginosa isolates, highest resistance (81.8%) was seen toward meropenem and piperacillin, 79.5% of Acinetobacter spp. showed resistance to aztreonam, while 93-100% of Klebsiella spp and E. coli displayed resistance to amoxyclavulanic acid, ceftriaxone, and ceftazidime. The proportion of extended-spectrum beta-lactamase producers among Enterobacteriaceae was 78.6%. There was a significant higher rate of infection with MDRGN organisms in pediatric patients with a higher percentage of total burn surface area (TBSA) than patients with lower TBSA (p = 0.016). CONCLUSIONS: P. aeruginosa, Acinetobacter spp., and Klebsiella spp. are the common Gram-negative pathogens causing burn wound infections in hospitalized pediatric patients in our setting. A high proportion of these organisms were multidrug resistant. The findings appeal for regular antimicrobial resistance surveillance in burn wound infection to inform empirical therapy.

Use of probiotics to reduce infections and death and prevent colonization with extended-spectrum beta-lactamase (ESBL)-producing bacteria among newborn infants in Tanzania (ProRIDE Trial): study protocol for a randomized controlled clinical trial.

BACKGROUND: Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) has emerged as an urgent global health threat and is by the World Health Organization ranked as priority 1 among pathogens in need of new treatment. Studies have shown high mortality in Tanzanian children with ESBL-E infections. Gut colonization of ESBL-E, which is a potential risk factor of ESBL-E infections, is reported to be very high among children in Tanzania. Probiotics may potentially reduce gut colonization of multidrug-resistant bacteria. However, there is limited data on whether probiotics may reduce ESBL-E carriage in infants. The ProRIDE Trial aims to evaluate whether the use of probiotics can reduce morbidity and mortality among infants in Haydom, Tanzania, and whether this effect is associated with a reduction in ESBL-E colonization and/or infections. METHODS/DESIGN: This large randomized double-blinded placebo-controlled trial aims to recruit 2000 newborn infants at Haydom Lutheran Hospital and the surrounding area in the period of November 2020 to November 2021. Participants will be enrolled from days 0 to 3 after birth and randomized to receive probiotics or placebo for 4 weeks. Participants will be followed-up for 6 months, during which three visits will be made to collect clinical and demographic information, as well as rectal swabs and fecal samples which will be subjected to laboratory analysis. The primary composite outcome is the prevalence of death and/or hospitalization at 6 months of age. DISCUSSION: As the use of probiotics may give a more favorable gut composition, and thereby improve health and reduce morbidity and mortality, the results may have implications for future therapy guidelines in Africa and internationally. TRIAL REGISTRATION: ClinicalTrials.gov NCT04172012. Registered on November 21, 2019.

Predominance of PVL-negative community-associated methicillin-resistant Staphylococcus aureus sequence type 8 in newly diagnosed HIV-infected adults, Tanzania.

Difficult-to-treat infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are of concern in people living with HIV infection as they are more vulnerable to infection. We aimed to identify molecular characteristics of MRSA colonizing newly diagnosed HIV-infected adults in Tanzania. Individuals newly diagnosed with HIV infection were recruited in Dar es Salaam, Tanzania, from April 2017 to May 2018, as part of the randomized clinical trial CoTrimResist ( ClinicalTrials.gov identifier: NCT03087890). Nasal/nasopharyngeal isolates of Staphylococcus aureus were susceptibility tested by disk diffusion method, and cefoxitin-resistant isolates were characterized by short-reads whole genome sequencing. Four percent (22/537) of patients carried MRSA in the nose/nasopharynx. MRSA isolates were frequently resistant towards gentamicin (95%), ciprofloxacin (91%), and erythromycin (82%) but less often towards trimethoprim-sulfamethoxazole (9%). Seventy-three percent had inducible clindamycin resistance. Erythromycin-resistant isolates harbored ermC (15/18) and LmrS (3/18) resistance genes. Ciprofloxacin resistance was mediated by mutations of the quinolone resistance-determining region (QRDR) sequence in the gyrA (S84L) and parC (S80Y) genes. All isolates belonged to the CC8 and ST8-SCCmecIV MRSA clone. Ninety-five percent of the MRSA isolates were spa-type t1476, and one exhibited spa-type t064. All isolates were negative for Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) type 1. All ST8-SCCmecIV-spa-t1476 MRSA clones from Tanzania were unrelated to the globally successful USA300 clone. Carriage of ST8 MRSA (non-USA300) was common among newly diagnosed HIV-infected adults in Tanzania. Frequent co-resistance to non-beta lactam antibiotics limits therapeutic options when infection occurs.

Molecular characterisation of the first New Delhi metallo-ß-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 (STs) and phylogenetic analysis was determined bioinformatically. RESULTS: Twelve A. baumannii were isolated from 2226 blood cultures, 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 ß-lactams, aminoglycosides and cotrimoxazole. CONCLUSIONS: This is the first report of New Delhi metallo-ß-lactamase-producing isolates of A. baumannii from Tanzania. The genetic context of blaNDM-1 provides further evidence of the importance of ISAba125 in 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.

High Prevalence of Fecal Carriage of Extended Spectrum ß-Lactamase-Producing Enterobacteriaceae Among Newly HIV-Diagnosed Adults in a Community Setting in Tanzania.

Colonization in HIV-infected populations with extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) is particularly worrisome in low-income settings. This study describes the prevalence of ESBL-PE carriage and associated risk factors among newly HIV-diagnosed adults in a community setting in Tanzania. A total of 595 newly diagnosed HIV adults with a median age of 35 years with interquartile range (IQR) 29-42 years and a median CD4 count of 492 cells/µL (IQR 390-666 cells/µL) were recruited. Among these, 194/595 (32.6%, 95% confidence interval [CI] 28.9-36.6) were ESBL-PE carriers. Participants with low CD4 count (<350 cells/µL) had significantly higher prevalence of ESBL-PE carriage compared with those with CD4 count ≥350 cells/µL (26/58, 44.8%, vs. 168/537, 31.3%, p = 0.04). Antibiotic use in last 4 weeks (odds ratio [OR] 1.55, 95% CI 1.08-2.22, p = 0.02) and CD4 count ≥350 cells/µL (OR 1.78, 95% CI 1.03-3.09, p = 0.04) were independent risk factors for fecal carriage of ESBL-PE. In total, 244 isolates of ESBL-PE were isolated from 194 participants. Of these, 238/244 (97.5%) harbored blaCTX-M genes, with blaCTX-M-15 being predominant (219/238 (92%), followed by blaCTX-M-27 (9/238 (3.8%), blaCTX-M-14 (8/238 (3.4%), blaCTX-M-55 (1/238), and blaCTX-M 211/3 (1/238). blaSHV-2a genes were detected in four isolates, whereas the blaSHV-12 gene was detected in one isolate. Phenotypic carbapenemase-producing Enterobacteriaceae was detected in one HIV-positive person with CD4 count 132 cells/µL. In conclusion prevalence of ESBL-PE carriage is high among newly diagnosed HIV adults in Dar es Salaam, and is significantly associated antibiotic use and low CD4 count.

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 bloodstream infections and malaria are major causes of death. METHODS: From March 2017 to July 2018, we enrolled 2,226 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, and we 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 (426/2,226) had pathogens detected from blood. Eleven percent (236/2,226) of the children had bacteraemia/fungaemia and 10% (204/2,063) 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 50% 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. falciparum in plasma. Overall, in-hospital death was 4% (89/2,146), 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). CONCLUSION: 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.