Influence of Stream-Subsurface Exchange Flux and Bacterial Biofilms on Oxygen Consumption Under Nutrient-Rich Conditions

The lack of a complete understanding of the complex reciprocal interactions between hydrological processes and the structure and function of microbial communities limits our ability to improve the predictions of microbial metabolism in streams. We report here on how overlying water velocity and losing and gaining flux interact with bacterial community structure and its activity to control oxygen consumption in a sandy streambed under high nutrient levels. We used an experimental flume packed with natural sediment and measured the bacterial biomass distribution and oxygen profiles in the streambed and across bed forms. Local oxygen consumption rates were calculated with a 1-D numerical model (GRADIENT). Bacterial abundance and production rates varied across the bed form within 1 order of magnitude, while their taxonomic classes were similar across bed forms despite variations in flow conditions and sediment disturbance events. However, bacterial production rates were not directly correlated with bacterial abundance. On the other hand, oxygen consumption rates ranged over 4 orders of magnitude across the bed forms and were highly correlated with the vertical exchange flux between the water and the streambed. The results strongly suggest that under high nutrient levels, the system is, in general, transport limited and that predicting oxygen consumption rates depends on local vertical exchange fluxes

Nitrogen and phosphorus limitation of oceanic microbial growth during spring in the Gulf of Aqaba

Bioassay experiments were performed to identify how growth of key groups within the microbial community was simultaneously limited by nutrient (nitrogen and phosphorus) availability during spring in the Gulf of Aqaba's oceanic waters. Measurements of chlorophyll a (chl a) concentration and fast repetition rate (FRR) fluorescence generally demonstrated that growth of obligate phototrophic phytoplankton was co-limited by N and P and growth of facultative aerobic anoxygenic photoheterotropic (AAP) bacteria was limited by N. Phytoplankton exhibited an increase in chl a biomass over 24 to 48 h upon relief of nutrient limitation. This response coincided with an increase in photosystem II (PSII) photochemical efficiency (F v /F m), but was preceded (within 24 h) by a decrease in effective absorption crosssection (σPSII) and electron turnover time (τ). A similar response for τ and bacterio-chl a was observed for the AAPs. Consistent with the up-regulation of PSII activity with FRR fluorescence were observations of newly synthesized PSII reaction centers via low temperature (77K) fluorescence spectroscopy for addition of N (and N + P). Flow cytometry revealed that the chl a and thus FRR fluorescence responses were partly driven by the picophytoplankton (æ10 μm) community, and in particular Synechococcus. Productivity of obligate heterotrophic bacteria exhibited the greatest increase in response to a natural (deep water) treatment, but only a small increase in response to N and P addition, demonstrating the importance of additional substrates (most likely dissolved organic carbon) in moderating the heterotrophs. These data support previous observations that the microbial community response (autotrophy relative to heterotrophy) is critically dependent upon the nature of transient nutrient enrichment. © Inter-Research 2009

Planktonic Aggregates as Hotspots for Heterotrophic Diazotrophy: The Plot Thickens

Biological dinitrogen (N-2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N-2 fixation by NCDs and propose a conceptual framework for aggregate-associated N-2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments

Vaccine Effectiveness against DS-1-Like Rotavirus Strains in Infants with Acute Gastroenteritis, Malawi, 2013-2015.

Atypical DS-1-like G1P[8] rotaviruses emerged in 2013 in Malawi after rotavirus vaccine introduction. Vaccine effectiveness among infants hospitalized with acute DS-1-like G1P[8] rotavirus gastroenteritis was 85.6% (95% CI 34.4%-96.8%). These findings suggest that vaccine provides protection against these strains despite their emergence coinciding with vaccine introduction

The quality and diagnostic value of open narratives in verbal autopsy: a mixed-methods analysis of partnered interviews from Malawi

Background Verbal autopsy (VA), the process of interviewing a deceased’s family or caregiver about signs and symptoms leading up to death, employs tools that ask a series of closed questions and can include an open narrative where respondents give an unprompted account of events preceding death. The extent to which an individual interviewer, who generally does not interpret the data, affects the quality of this data, and therefore the assigned cause of death, is poorly documented. We aimed to examine inter-interviewer reliability of open narrative and closed question data gathered during VA interviews. Methods During the introduction of VA data collection, as part of a larger study in Mchinji district, Malawi, we conducted partner interviews whereby two interviewers independently recorded open narrative and closed questions during the same interview. Closed questions were collected using a smartphone application (mobile-InterVA) and open narratives using pen and paper. We used mixed methods of analysis to evaluate the differences between recorded responses to open narratives and closed questions, causes of death assigned, and additional information gathered by open narrative. Results Eighteen partner interviews were conducted, with complete data for 11 pairs. Comparing closed questions between interviewers, the median number of differences was 1 (IQR: 0.5–3.5) of an average 65 answered; mean inter-interviewer concordance was 92 % (IQR: 92–99 %). Discrepancies in open narratives were summarized in five categories: demographics, history and care-seeking, diagnoses and symptoms, treatment and cultural. Most discrepancies were seen in the reporting of diagnoses and symptoms (e.g., malaria diagnosis); only one pair demonstrated no clear differences. The average number of clinical symptoms reported was 9 in open narratives and 20 in the closed questions. Open narratives contained additional information on health seeking and social issues surrounding deaths, which closed questions did not gather. Conclusions The information gleaned during open narratives was subject to inter-interviewer variability and contained a limited number of symptom indicators, suggesting that their use for assigning cause of death is questionable. However, they contained rich information on care-seeking, healthcare provision and social factors in the lead-up to death, which may be a valuable source of information for promoting accountable health services

Improving Aboriginal maternal and infant health services in the \u27Top End\u27 of Australia; synthesis of the findings of a health services research program aimed at engaging stakeholders, developing research capacity and embedding change

BackgroundHealth services research is a well-articulated research methodology and can be a powerful vehicle to implement sustainable health service reform. This paper presents a summary of a five-year collaborative program between stakeholders and researchers that led to sustainable improvements in the maternity services for remote-dwelling Aboriginal women and their infants in the Top End (TE) of Australia. MethodsA mixed-methods health services research program of work was designed, using a participatory approach. The study area consisted of two large remote Aboriginal communities in the Top End of Australia and the hospital in the regional centre (RC) that provided birth and tertiary care for these communities. The stakeholders included consumers, midwives, doctors, nurses, Aboriginal Health Workers (AHW), managers, policy makers and support staff. Data were sourced from: hospital and health centre records; perinatal data sets and costing data sets; observations of maternal and infant health service delivery and parenting styles; formal and informal interviews with providers and women and focus groups. Studies examined: indicator sets that identify best care, the impact of quality of care and remoteness on health outcomes,  discrepancies in the birth counts in a range of different data sets and ethnographic studies of ‘out of hospital’ or health centre birth and parenting. A new model of maternity care was introduced by the health service aiming to improve care following the findings of our research. Some of these improvements introduced during the five-year research program of research were evaluated. ResultsCost effective improvements were made to the acceptability, quality and outcomes of maternity care. However, our synthesis identified system-wide problems that still account for poor quality of infant services, specifically, unacceptable standards of infant care and parent support, no apparent relationship between volume and acuity of presentations and staff numbers with the required skills for providing care for infants, and an ‘outpatient’ model of care. Services were also characterised by absent Aboriginal leadership and inadequate coordination between remote and tertiary services that is essential to improve quality of care and reduce ‘system-introduced’ risk. ConclusionEvidence-informed redesign of maternity services and delivery of care has improved clinical effectiveness and quality for women. However, more work is needed to address substandard care provided for infants and their parents

Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998-2016): a surveillance study.

BACKGROUND Bacterial bloodstream infection is a common cause of morbidity and mortality in sub-Saharan Africa, yet few facilities are able to maintain long-term surveillance. The Malawi-Liverpool-Wellcome Trust Clinical Research Programme has done sentinel surveillance of bacteraemia since 1998. We report long-term trends in bloodstream infection and antimicrobial resistance from this surveillance. METHODS In this surveillance study, we analysed blood cultures that were routinely taken from adult and paediatric patients with fever or suspicion of sepsis admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi from 1998 to 2016. The hospital served an urban population of 920 000 in 2016, with 1000 beds, although occupancy often exceeds capacity. The hospital admits about 10 000 adults and 30 000 children each year. Antimicrobial susceptibility tests were done by the disc diffusion method according to British Society of Antimicrobial Chemotherapy guidelines. We used the Cochran-Armitage test for trend to examine trends in rates of antimicrobial resistance, and negative binomial regression to examine trends in icidence of bloodstream infection over time. FINDINGS Between Jan 1, 1998, and Dec 31, 2016, we isolated 29 183 pathogens from 194 539 blood cultures. Pathogen detection decreased significantly from 327·1/100 000 in 1998 to 120·2/100 000 in 2016 (p<0·0001). 13 366 (51·1%) of 26 174 bacterial isolates were resistant to the Malawian first-line antibiotics amoxicillin or penicillin, chloramphenicol, and co-trimoxazole; 68·3% of Gram-negative and 6·6% of Gram-positive pathogens. The proportions of non-Salmonella Enterobacteriaceae with extended spectrum beta-lactamase (ESBL) or fluoroquinolone resistance rose significantly after 2003 to 61·9% in 2016 (p<0·0001). Between 2003 and 2016, ESBL resistance rose from 0·7% to 30·3% in Escherichia coli, from 11·8% to 90·5% in Klebsiella spp and from 30·4% to 71·9% in other Enterobacteriaceae. Similarly, resistance to ciprofloxacin rose from 2·5% to 31·1% in E coli, from 1·7% to 70·2% in Klebsiella spp and from 5·9% to 68·8% in other Enterobacteriaceae. By contrast, more than 92·0% of common Gram-positive pathogens remain susceptible to either penicillin or chloramphenicol. Meticillin-resistant Staphylococcus aureus (MRSA) was first reported in 1998 at 7·7% and represented 18·4% of S aureus isolates in 2016. INTERPRETATION The rapid expansion of ESBL and fluoroquinolone resistance among common Gram-negative pathogens, and the emergence of MRSA, highlight the growing challenge of bloodstream infections that are effectively impossible to treat in this resource-limited setting. FUNDING Wellcome Trust, H3ABionet, Southern Africa Consortium for Research Excellence (SACORE)

Use of health services by remote dwelling Aboriginal infants in tropical northern Australia: a retrospective cohort study

<p>Abstract</p> <p>Background</p> <p>Australia is a wealthy developed country. However, there are significant disparities in health outcomes for Aboriginal infants compared with other Australian infants. Health outcomes tend to be worse for those living in remote areas. Little is known about the health service utilisation patterns of remote dwelling Aboriginal infants. This study describes health service utilisation patterns at the primary and referral level by remote dwelling Aboriginal infants from northern Australia.</p> <p>Results</p> <p>Data on 413 infants were analysed. Following birth, one third of infants were admitted to the regional hospital neonatal nursery, primarily for preterm birth. Once home, most (98%) health service utilisation occurred at the remote primary health centre, infants presented to the centre about once a fortnight (mean 28 presentations per year, 95%CI 26.4-30.0). Half of the presentations were for new problems, most commonly for respiratory, skin and gastrointestinal symptoms. Remaining presentations were for reviews or routine health service provision. By one year of age 59% of infants were admitted to hospital at least once, the rate of hospitalisation per infant year was 1.1 (95%CI 0.9-1.2).</p> <p>Conclusions</p> <p>The hospitalisation rate is high and admissions commence early in life, visits to the remote primary health centre are frequent. Half of all presentations are for new problems. These findings have important implications for health service planning and delivery to remote dwelling Aboriginal families.</p

Bacterial Meningitis in Malawian Adults, Adolescents, and Children During the Era of Antiretroviral Scale-up and Haemophilus influenzae Type b Vaccination, 2000-2012

Background We documented bacterial meningitis trends among adults and children presenting to a large teaching hospital in Malawi during introduction of Haemophilus influenzae type b (Hib) vaccination and the rollout of antiretroviral therapy (ART). Methods We analyzed data from 51 000 consecutive cerebrospinal fluid (CSF) samples obtained from adults, adolescents, and children with suspected meningitis admitted to the Queen Elizabeth Central Hospital, Blantyre, Malawi, between 2000 and 2012. Results There was a significant decline in the total number of CSF isolates over 12 years (incident rate ratio [IRR], 0.93; 95% CI, .92–.94; P < .001). This decline was entirely in children aged <5 years (IRR, 0.87; 95% CI, .85–.88; P < .001) and coincided with the introduction of Hib vaccination. The number of adult isolates has remained unchanged (IRR, 0.99; 95% CI, .97–1.0; P = .135) despite rapid scale-up of ART provision. In children aged <5 years, Streptococcus pneumoniae, nontyphoidal salmonellae (NTS), and Hib were the most frequently isolated pathogens, and have declined over this time period. Streptococcus pneumoniae was the most frequently isolated pathogen in older children and adults. Estimated incidence of bacterial meningitis in 2012 was 20 per 100 000 cases in children aged <14 years, 6 per 100 000 adolescents, and 10 per 100 000 adults. Conclusions Rates of bacterial meningitis have declined in children, but not adults, coinciding with the introduction of Hib vaccination. The highly successful rollout of ART has not yet resulted in a reduction in the incidence in adults where the burden remains high. Long-term surveillance of bacterial meningitis outside of the epidemic “meningitis belt” in Africa is essential

Duration and Density of Fecal Rotavirus Shedding in Vaccinated Malawian Children With Rotavirus Gastroenteritis.

Quantifying rotavirus shedding among vaccinated individuals will aid understanding of vaccine indirect effects. Serial stool samples were collected from 196 children who presented with rotavirus gastroenteritis to health facilities in Blantyre, Malawi, and were tested for rotavirus using a VP6 semi-quantitative, real-time polymerase chain reaction. The median duration of fecal shedding was 28 days (95% CI, 19-28). The median copy numbers for peak shedding were 1.99 × 107 (interquartile range, 3.39 × 106 to 6.37 × 107). The fecal viral load was positively associated with disease severity and negatively associated with serum anti-rotavirus immunoglobin A. High and persistent rotavirus shedding among vaccinated children with breakthrough disease may contribute to ongoing transmission in this setting