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Introduction: Carbapenem-resistant Enterobacteriaceae are emerging as a global public-health threat and cause substantial challenges in clinical practice. \ud 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.\ud Aim: To describe the resistance mechanisms of carbapenem-resistant Escherichia coli. \ud 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 fecal carriage of carbapenamases and OXA-48 producing 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. \ud Results: Three carbapenem-resistant E. coli were detected, two from neonates and one from an HIV infected adult. All three isolates carried blaNDM-5. Two E. coli from neonates belong to ST167 and blaNDM-5 co-existed with blaCTX-M-15 and blaOXA-01, and all were carried on IncFIA type plasmids. The E. coli from the HIV infected adult belongs to ST2083, and carried blaNDM-5 on an IncX3 type plasmid and blaCMY-42 on an IncI type plasmid. All blaNDM-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 harbored 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.\ud Conclusion: This is the first report from Tanzania detecting blaNDM-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.

Antimicrobial resistance genes (ARGs) are often associated with mobile genetic elements (MGEs), which facilitate their movement within and between bacterial populations. Detection of mobility is therefore important to understand the dynamics of MGE dissemination and their associated genes, especially in resistant clinical isolates that often have multiple ARGs associated with MGEs. Therefore, this study aimed to develop an entrapment vector to capture active MGEs and ARGs in clinical isolates of Escherichia coli.

Additional file 2. Letter of ethical review REC West.

Additional file 4. Tildeling av Helse Vests forskingsmidlar 2019 - Åpen prosjektstøtte.

Additional file 3. Re: ethical clearance certificate for conducting medical research in Tanzania.

Additional file 5. Letter of financial support.

Diarrheal diseases are a leading cause of morbidity and mortality worldwide, but the etiology of diarrhea and its relation to nutritional outcomes in resource-limited settings is poorly defined. We sought to determine the etiology of community-acquired diarrhea in Tanzanian infants and to assess the association with anthropometrics and novel intestinal biomarkers.A convenience sample of infants in a trial of zinc and/or multivitamin supplementation in Tanzania was selected. Subjects were enrolled at age 6 weeks and studied for 18 months. Stool samples were obtained from children with acute diarrhea. A novel, polymerase chain reaction-based TaqMan array was used to screen stool for 15 enteropathogens. A subset of subjects had serum gastrointestinal biomarkers measured.One hundred twenty-three subjects with diarrhea were enrolled. The mean ± SD age at stool sample collection was 12.4 ± 3.9 months. Thirty-five enteropathogens were identified in 34 (27.6%) subjects: 11 rotavirus, 9 Cryptosporidium spp, 7 Shigella spp, 3 Campylobacter jejuni/coli, 3 heat stable-enterotoxigenic Escherichia coli, and 2 enteropathogenic E coli. Subjects with any identified enteropathogen had significantly lower weight-for-length z scores (-0.55 ± 1.10 vs 0.03 ± 1.30, P = 0.03) at the final clinic visit than those without an identified pathogen. Fifty of the 123 subjects (40.7%) had serum analyzed for antibodies to lipopolysaccharide (LPS) and flagellin. Subjects with any identified enteropathogen had lower immunoglobulin (IgA) antibodies to LPS (0.75 ± 0.27 vs 1.13 ± 0.77, P = 0.01) and flagellin (0.52 ± 0.16 vs 0.73 ± 0.47, P = 0.02) than those without an identified pathogen.This quantitative polymerase chain reaction method may allow identification of enteropathogens that place children at higher risk for suboptimal growth. IgA anti-LPS and flagellin antibodies hold promise as emerging intestinal biomarkers.

Antimicrobial resistance pattern of isolates from Hospital-acquired and Community-acquired urinary tract infections (% of resistance isolates within each group). (DOC 52 kb)

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.

Introduction: Diarrhoeal disease is one of the leading causes of illness and death in children below five years, especially in developing countries. It is estimated to cause 0.7 million deaths among children younger than 5 years of age, most of which occur in children below two years age. Viruses such as rotavirus, norovirus and adenovirus are known to be major causes of infectious diarrhoea. Objectives: This study was done investigate the molecular epidemiology of rotavirus, norovirus and adenovirus and their association with demographic and clinical parameters including HIV and in children under two years of age in Dar es Salaam, Tanzania. Methods: This was a case control study conducted in Tanzania between August 2010 and July 2011. Cases were children admitted due to diarrhoea at three major hospitals of Dar es Salaam. Controls were children without history of diarrhoea for one month prior the study. These were either attending child health clinics for immunisation and growth monitoring or admitted due to diseases other than diarrhoea. Questionnaires were used to obtain demographic and clinical information. Stool specimens were collected from each study participant. We used ELISA methods for detection of rotavirus and adenovirus from stool specimens. Real time PCR was used for detection of norovirus. PCR followed by sequencing were used for typing all the three viruses. Results: Viruses were detected in nearly half (48.8%) of the cases and in 17.5% of the controls. Dual viral infection was found in 7.4% and 8.1% in cases and controls respectively. Among cases, rotavirus was the most common detected virus (32.5%) followed by norovirus (18.3%), and adenovirus (3.5%). In controls the prevalence of rotavirus, norovirus and adenovirus was 7.7%, 9.2% and 2.4% respectively. The peak prevalence of virus infection in cases was seen in the age group 7-12 months, 52.0%. Rotavirus G1P[8] predominated in cases and controls. Norovirus GII.4 predominated both in cases (87.9%) and controls (56.5%). Enteric adenoviruses contributed 50% in cases and 46% in controls. Rotavirus was more prevalent during cold than hot months during the study period. Rotavirus infection was significantly lower in HIV infected (15.4%) than HIV uninfected children (55.3%). There were no significant associations between HIV and either norovirus or adenovirus infection. There were no significant differences observed between viral infection and gender or parent level of education. Conclusion: Viruses contribute to a high burden of diarrhoea in hospitalised children of Dar es Salaam, Tanzania. We found a high frequency of asymptomatic carriage of diarrhoea-associated viruses in healthy children; these children may be a source of infection in the community. We observed a large genetic diversity of the three viruses investigated in this study. Pre-rotavirus vaccination data showed predominance of rotavirus genotype G1. Our study suggests that rotavirus may not be an opportunistic pathogen in children infected with HIV.