A call for antibiotic alternatives research

The persistence and spread of antibiotic resistance, in conjunction with decreased profitability of new antibiotics, have created the dangerous prospect of ineffective therapies against bacterial diseases. National strategies aimed at discovery, development, and definition of the mechanisms of effective antibiotic alternatives, especially for agricultural applications, should be encouraged

Estimation of viral richness from shotgun metagenomes using a frequency count approach

BACKGROUND: Viruses are important drivers of ecosystem functions, yet little is known about the vast majority of viruses. Viral shotgun metagenomics enables the investigation of broad ecological questions in phage communities. One ecological characteristic is species richness, which is the number of different species in a community. Viruses do not have a phylogenetic marker analogous to the bacterial 16S rRNA gene with which to estimate richness, and so contig spectra are employed to measure the number of virus taxa in a given community. A contig spectrum is generated from a viral shotgun metagenome by assembling the random sequence reads into groups of sequences that overlap (contigs) and counting the number of sequences that group within each contig. Current tools available to analyze contig spectra to estimate phage richness are limited by relying on rank-abundance data. RESULTS: We present statistical estimates of virus richness from contig spectra. The program CatchAll (http://www.northeastern.edu/catchall/) was used to analyze contig spectra in terms of frequency count data rather than rank-abundance, thus enabling formal statistical analyses. Also, the influence of potentially spurious low-frequency counts on richness estimates was minimized by two methods, empirical and statistical. The results show greater estimates of viral richness than previous calculations in nearly all environments analyzed, including swine feces and reclaimed fresh water. CONCLUSIONS: CatchAll yielded consistent estimates of richness across viral metagenomes from the same or similar environments. Additionally, analysis of pooled viral metagenomes from different environments via mixed contig spectra resulted in greater richness estimates than those of the component metagenomes. Using CatchAll to analyze contig spectra will improve estimations of richness from viral shotgun metagenomes, particularly from large datasets, by providing statistical measures of richness

High ANC coverage and low skilled attendance in a rural Tanzanian district: a case for implementing a birth plan intervention

BACKGROUND: In Tanzania, more than 90% of all pregnant women attend antenatal care at least once and approximately 62% four times or more, yet less than five in ten receive skilled delivery care at available health units. We conducted a qualitative study in Ngorongoro district, Northern Tanzania, in order to gain an understanding of the health systems and socio-cultural factors underlying this divergent pattern of high use of antenatal services and low use of skilled delivery care. Specifically, the study examined beliefs and behaviors related to antenatal, labor, delivery and postnatal care among the Maasai and Watemi ethnic groups. The perspectives of health care providers and traditional birth attendants on childbirth and the factors determining where women deliver were also investigated. METHODS: Twelve key informant interviews and fifteen focus group discussions were held with Maasai and Watemi women, traditional birth attendants, health care providers, and community members. Principles of the grounded theory approach were used to elicit and assess the various perspectives of each group of participants interviewed. RESULTS: The Maasai and Watemi women's preferences for a home birth and lack of planning for delivery are reinforced by the failure of health care providers to consistently communicate the importance of skilled delivery and immediate post-partum care for all women during routine antenatal visits. Husbands typically serve as gatekeepers of women's reproductive health in the two groups - including decisions about where they will deliver- yet they are rarely encouraged to attend antenatal sessions. While husbands are encouraged to participate in programs to prevent maternal-to-child transmission of HIV, messages about the importance of skilled delivery care for all women are not given emphasis. CONCLUSIONS: Increasing coverage of skilled delivery care and achieving the full implementation of Tanzania's Focused Antenatal Care Package in Ngorongoro depends upon improved training and monitoring of health care providers, and greater family participation in antenatal care visits

Still too far to walk: Literature review of the determinants of delivery service use

BACKGROUND: Skilled attendance at childbirth is crucial for decreasing maternal and neonatal mortality, yet many women in low- and middle-income countries deliver outside of health facilities, without skilled help. The main conceptual framework in this field implicitly looks at home births with complications. We expand this to include "preventive" facility delivery for uncomplicated childbirth, and review the kinds of determinants studied in the literature, their hypothesized mechanisms of action and the typical findings, as well as methodological difficulties encountered. METHODS: We searched PubMed and Ovid databases for reviews and ascertained relevant articles from these and other sources. Twenty determinants identified were grouped under four themes: (1) sociocultural factors, (2) perceived benefit/need of skilled attendance, (3) economic accessibility and (4) physical accessibility. RESULTS: There is ample evidence that higher maternal age, education and household wealth and lower parity increase use, as does urban residence. Facility use in the previous delivery and antenatal care use are also highly predictive of health facility use for the index delivery, though this may be due to confounding by service availability and other factors. Obstetric complications also increase use but are rarely studied. Quality of care is judged to be essential in qualitative studies but is not easily measured in surveys, or without linking facility records with women. Distance to health facilities decreases use, but is also difficult to determine. Challenges in comparing results between studies include differences in methods, context-specificity and the substantial overlap between complex variables. CONCLUSION: Studies of the determinants of skilled attendance concentrate on sociocultural and economic accessibility variables and neglect variables of perceived benefit/need and physical accessibility. To draw valid conclusions, it is important to consider as many influential factors as possible in any analysis of delivery service use. The increasing availability of georeferenced data provides the opportunity to link health facility data with large-scale household data, enabling researchers to explore the influences of distance and service quality

Determinants of health facility utilization for childbirth in rural western Kenya: cross-sectional study

Background: Skilled attendance at delivery is recognized as one of the most important factors in preventing maternal death. However, more than 50% of births in Kenya still occur in non-institutional locations supported by family members and/or traditional birth attendants (TBAs). To improve this situation, a study of the determinants of facility delivery, including individual, family and community factors, was necessary to consider effective intervention in Kenya.Methods: This study was conducted to identify the factors which influence the place of delivery in rural western Kenya, and to recommend ways to improve women\u27s access to skilled attendants at delivery. A community-based cross-sectional survey was carried out from August to September 2011 in all 64 sub-locations which were covered by community health workers (CHWs). An interviewer-administered questionnaire on seventeen comprehensive variables was administered to 2,560 women who had children aged 12-24 months.Results: The response rate was 79% (n = 2,026). Of the respondents, 48% of births occurred in a health facility and 52% in a non-institutional location. The significant determinants of facility delivery examined using multivariate analysis were: maternal education level, maternal health knowledge, ANC visits, birth interval, economic status of household, number of household members, household sanitation practices and traveling time to nearest health facility.Conclusions: The results suggest that the involvement of TBAs to promote facility delivery is still one of the most important strategies. Strengthening CHWs\u27 performance by focusing on a limited number of topics and clear management guidance might also be an effective intervention. Stressing the importance of regular attendance at ANC (at least four times) would be effective in enhancing motivation for a facility delivery. Based on our findings, those actions to improve the facility delivery rate should focus more on pregnant women who have a low education level, poor health knowledge and short pregnancy spacing. In addition, women with low economic status, a large number of family members and a long distance to travel to a health facility should also be targeted by further interventions

Isolation of Tetracycline-Resistant Megasphaera elsdenii Strains with Novel Mosaic Gene Combinations of tet(O) and tet(W) from Swine

Anaerobic bacteria insensitive to chlortetracycline (64 to 256 μg/ml) were isolated from cecal contents and cecal tissues of swine fed or not fed chlortetracycline. A nutritionally complex, rumen fluid-based medium was used for culturing the bacteria. Eight of 84 isolates from seven different animals were identified as Megasphaera elsdenii strains based on their large-coccus morphology, rapid growth on lactate, and 16S ribosomal DNA sequence similarities with M. elsdenii LC-1(T). All eight strains had tetracycline MICs of between 128 and 256 μg/ml. Based on PCR assays differentiating 14 tet classes, the strains gave a positive reaction for the tet(O) gene. By contrast, three ruminant M. elsdenii strains recovered from 30-year-old culture stocks had tetracycline MICs of 4 μg/ml and did not contain tet genes. The tet genes of two tetracycline-resistant M. elsdenii strains were amplified and cloned. Both genes bestowed tetracycline resistance (MIC = 32 to 64 μg/ml) on recombinant Escherichia coli strains. Sequence analysis revealed that the M. elsdenii genes represent two different mosaic genes formed by interclass (double-crossover) recombination events involving tet(O) and tet(W). One or the other genotype was present in each of the eight tetracycline-resistant M. elsdenii strains isolated in these studies. These findings suggest a role for commensal bacteria not only in the preservation and dissemination of antibiotic resistance in the intestinal tract but also in the evolution of resistance