The person-to-person transmission landscape of the gut and oral microbiomes.

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

How has mass drug administration with dihydroartemisinin-piperaquine impacted molecular markers of drug resistance? A systematic review.

The World Health Organization (WHO) recommends surveillance of molecular markers of resistance to anti-malarial drugs. This is particularly important in the case of mass drug administration (MDA), which is endorsed by the WHO in some settings to combat malaria. Dihydroartemisinin-piperaquine (DHA-PPQ) is an artemisinin-based combination therapy which has been used in MDA. This review analyses the impact of MDA with DHA-PPQ on the evolution of molecular markers of drug resistance. The review is split into two parts. Section I reviews the current evidence for different molecular markers of resistance to DHA-PPQ. This includes an overview of the prevalence of these molecular markers in Plasmodium falciparum Whole Genome Sequence data from the MalariaGEN Pf3k project. Section II is a systematic literature review of the impact that MDA with DHA-PPQ has had on the evolution of molecular markers of resistance. This systematic review followed PRISMA guidelines. This review found that despite being a recognised surveillance tool by the WHO, the surveillance of molecular markers of resistance following MDA with DHA-PPQ was not commonly performed. Of the total 96 papers screened for eligibility in this review, only 20 analysed molecular markers of drug resistance. The molecular markers published were also not standardized. Overall, this warrants greater reporting of molecular marker prevalence following MDA implementation. This should include putative pfcrt mutations which have been found to convey resistance to DHA-PPQ in vitro.

Prevalence of and risk factors for curable sexually transmitted infections on Bubaque Island, Guinea Bissau.

OBJECTIVES: Complications from sexually transmitted infections (STIs) can result in severe morbidity and mortality. To date, no STI population studies have been conducted on the Bijagos Islands, Guinea Bissau. Our objective was to estimate the prevalence of and identify risk factors for Chlamydia trachomatis (Ct), Neisseria gonorrhoea (Ng), Mycoplasma genitalium (Mg), Trichomonas vaginalis (Tv) and Treponema pallidum (Tp) on Bubaque, the most populated island. METHODS: A cross-sectional survey was conducted on the island of Bubaque among people aged 16-49 years. Participants were asked to answer a questionnaire on STI risk factors, to provide urine samples (men and women) and vaginal swabs (women) for PCR testing for Ct, Ng, Mg and Tv, and to provide dry blood spots for Tp particle agglutination assays. Data were analysed to estimate the prevalence of STIs and logistic regression was used to identify risk factors. RESULTS: In total, 14.9% of participants were found to have a curable STI, with the highest prevalence being observed for Tv (5.9%) followed by Ct (3.8%), Ng (3.8%), Mg (1.9%) and Tp (0.8%). Significant risk factors for having any STI included being female, younger age and concurrent partnership. Having had a previous STI that was optimally treated was a protective factor. CONCLUSIONS: This study demonstrates that there is a considerable burden of STI on the Bijagos Islands, stressing the need for diagnostic testing to facilitate early detection and treatment of these pathogens to stop ongoing transmission. Moreover, these results indicate the need to conduct further research into the STI burden on the Bijagos Islands to help inform and develop a national STI control strategy.

A survey of knowledge, attitudes and practices regarding malaria and bed nets on Bubaque Island, Guinea-Bissau.

BACKGROUND: Malaria remains a significant public health problem in Guinea-Bissau, West Africa. Government control measures include bed net distribution campaigns, however, local knowledge, attitudes and practices towards bed nets and malaria are uncharacterized on the remote Bijagos Archipelago. METHODS: Knowledge, attitude and practice questionnaires were conducted with household heads, aiming to explore the understanding of malaria and factors influencing bed net uptake and usage. Nets were observed in situ to appraise net quality and behaviour. All 14 villages and one semi-urban neighbourhood on Bubaque Island were included. One in 5 households containing school-aged children were randomly selected. RESULTS: Of 100 participants, 94 were aware of malaria and 66 of those considered it a significant or severe problem, primarily because of its impact on health and income. Transmission, symptoms and risk factors were well known, however, 28.0% of participants felt under-informed. Some 80.0% reported contact with distribution campaigns, with inter-village variability. Campaign contact was associated with feeling well informed (OR 3.44; P = 0.024) and inversely with perceiving malaria a household (OR 0.18; P = 0.002) or regional problem (OR 0.25; P = 0.018). Every household contained nets; every identifiable example was a long-lasting insecticide-treated net (LLIN), however, 23.0% of households contained at least one expired net. Replacements were in demand; 89.0% of households reported that all residents used nets, and average occupancy was 2.07 people per net; 65.2% stated that the repurposing of bed nets was common. Correctly using bed nets, defined by age, integrity and demonstration, was 35.0% and strongly associated with completing intermittent preventative treatment in pregnancy (RR 3.63; P = 0.014). CONCLUSIONS: Knowledge of malaria is good in these communities. Bed nets are used widely and are valued for their role in preventing malaria. However, their use is frequently sub-optimal and offers a target for improving malaria control by adapting popular distribution campaigns to provide more education alongside fresh LLINs. The impact of this could be significant as LLINs represent the mainstay of malaria prevention in Guinea-Bissau; however, the persistence of malaria despite the high uptake of LLINs seen in this study suggests that novel supplementary approaches must also be considered.

A survey of Anopheles species composition and insecticide resistance on the island of Bubaque, Bijagos Archipelago, Guinea-Bissau.

BACKGROUND: Bubaque is the most populous island of the Bijagos archipelago, a group of malaria-endemic islands situated off the coast of Guinea-Bissau, West Africa. Malaria vector control on Bubaque relies almost exclusively on the use of long-lasting insecticidal nets (LLINs). However, there is little information on local vector bionomics and insecticide resistance. METHODS: A survey of mosquito species composition was performed at the onset of the wet season (June/July) and the beginning of the dry season (November/December). Sampling was performed using indoor adult light-traps and larval dipping. Anopheles mosquitoes were identified to species level and assessed for kdr allele frequency by TaqMan PCR. Females were analysed for sporozoite positivity by CSP-ELISA. Resistance to permethrin and α-cypermethrin was measured using the CDC-bottle bioassay incorporating the synergist piperonyl-butoxide. RESULTS: Several Anopheles species were found on the island, all belonging to the Anopheles gambiae sensu lato (s.l.) complex, including An. gambiae sensu stricto, Anopheles coluzzii, Anopheles melas, and An. gambiae/An. coluzzii hybrids. Endophagic Anopheles species composition and abundance showed strong seasonal variation, with a majority of An. gambiae (50% of adults collected) caught in June/July, while An. melas was dominant in November/December (83.9% of adults collected). Anopheles gambiae had the highest sporozoite rate in both seasons, with infection rates of 13.9% and 20% in June/July and November/December, respectively. Moderate frequencies of the West African kdr allele were found in An. gambiae (36%), An. coluzzii (35%), An. gambiae/An. coluzzii hybrids (42%). Bioassays suggest moderate resistance to α-cypermethrin, but full susceptibility to permethrin. CONCLUSIONS: The island of Bubaque maintained an An. gambiae s.l. population in both June/July and November/December. Anopheles gambiae was the primary vector at the onset of the wet season, while An. melas is likely to be responsible for most dry season transmission. There was moderate kdr allele frequency and synergist assays suggest likely metabolic resistance, which could reduce the efficacy of LLINs. Future control of malaria on the islands should consider the seasonal shift in mosquito species, and should employ continuous monitoring for insecticide resistance.

Population-based prevalence survey of follicular trachoma and trachomatous trichiasis in the Casamance region of Senegal.

BACKGROUND: Trachoma, caused by ocular infection with Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. We conducted the first population-based trachoma prevalence survey in the Casamance region of Senegal to enable the Senegalese National Eye Care Programme (NECP) to plan its trachoma control activities. The World Health Organization (WHO) guidelines state that any individual with trachomatous trichiasis (TT) should be offered surgery, but that surgery should be prioritised where the prevalence is >0.1%, and that districts and communities with a trachomatous inflammation, follicular (TF) prevalence of ≥10% in 1-9 year-olds should receive mass antibiotic treatment annually for a minimum of three years, along with hygiene promotion and environmental improvement, before re-assessing the prevalence to determine whether treatment can be discontinued (when TF prevalence in 1-9 year-olds falls <5%). METHODS: Local healthcare workers conducted a population-based household survey in four districts of the Bignona Department of Casamance region to estimate the prevalence of TF in 1-9 year-olds, and TT in ≥15 year-olds. Children's facial cleanliness (ocular and/or nasal discharge, dirt on the face, flies on the face) was measured at time of examination. Risk factor questionnaires were completed at the household level. RESULTS: Sixty communities participated with a total censused population of 5580 individuals. The cluster-, age- and sex-adjusted estimated prevalence of TF in 1-9 year-olds was 2.5% (95% Confidence Interval (CI) 1.8-3.6) (38/1425) at the regional level and <5% in all districts, although the upper 95%CI exceeded 5% in all but one district. The prevalence of TT in those aged ≥15 years was estimated to be 1.4% (95%CI 1.0-1.9) (40/2744) at the regional level and >1% in all districts. CONCLUSION: With a prevalence <5%, TF does not appear to be a significant public health problem in this region. However, TF monitoring and surveillance at sub-district level will be required to ensure that elimination targets are sustained and that TF does not re-emerge as a public health problem. TT surgery remains the priority for trachoma elimination efforts in the region, with an estimated 1819 TT surgeries to conduct.

Differential frequency of NKG2C/KLRC2 deletion in distinct African populations and susceptibility to Trachoma: a new method for imputation of KLRC2 genotypes from SNP genotyping data.

NKG2C is an activating receptor that is preferentially expressed on natural killer (NK) cells. The gene encoding NKG2C (killer cell lectin-like receptor C2, KLRC2) is present at different copy numbers in the genomes of different individuals. Deletion at the NKG2C locus was investigated in a case-control study of 1522 individuals indigenous to East- and West-Africa and the association with the ocular Chlamydia trachomatis infection and its sequelae was explored. The frequency of homozygous KLRC2 deletion was 13.7 % in Gambians and 4.7 % in Tanzanians. A significantly higher frequency of the deletion allele was found in West-Africans from the Gambia and Guinea-Bissau (36.2 % p = 2.105 × 10(-8), 26.8 % p = 0.050; respectively) in comparison to East-African Tanzanians where the frequency of the deletion is comparable to other human populations (20.9 %). We found no evidence for an association between the numbers of KLRC2 gene copies and the clinical manifestations of trachoma (follicular trachoma or conjunctival scarring). A new method for imputation of KLRC2 genotypes from single nucleotide polymorphism (SNP) data in 2621 individuals from the Gambia further confirmed these results. Our data suggest that NKG2C does not play a major role in trachomatous disease. We found that the deletion allele is present at different frequencies in different populations but the reason behind these differences is currently not understood. The new method offers the potential to use SNP arrays from genome wide association studies to study the frequency of KLRC2 deletion in other populations and its association with other diseases.

Inverse relationship between microRNA-155 and -184 expression with increasing conjunctival inflammation during ocular Chlamydia trachomatis infection.

BACKGROUND: Trachoma, a preventable blinding eye disease, is initiated by ocular infection with Chlamydia trachomatis (Ct). We previously showed that microRNAs (miR) -147b and miR-1285 were up-regulated in inflammatory trachomatous scarring. During the initial stage of disease, follicular trachoma with current Ct infection, the differential expression of miR has not yet been investigated. METHODS: Conjunctival samples were collected from 163 children aged 1-9 years old living in a trachoma-endemic region of Guinea Bissau, West Africa. Small RNA sequencing (RNAseq) was carried out on samples from five children with follicular trachoma and current Ct infection and five children with healthy conjunctivae and no Ct infection. Small RNAseq was also carried out on human epithelial cell lines infected with ocular Ct strains A2497 and isogenic plasmid-free A2497 in vitro. Results were validated by quantitative PCR (qPCR) in 163 clinical samples. RESULTS: Differential expression of RNAseq data identified 12 miR with changes in relative expression during follicular trachoma, of which 9 were confirmed as differentially expressed by qPCR (miR-155, miR-150, miR-142, miR-181b, miR-181a, miR-342, miR-132, miR-4728 and miR-184). MiR-155 and miR-184 expression had a direct relationship with the degree of clinical inflammation. MiR-155 was up-regulated (OR = 2.533 ((95 % CI = 1.291-4.971); P = 0.0069) and miR-184 was down-regulated (OR = 0.416 ((95 % CI = 0.300-0.578); P = 1.61*10(-7)) as the severity of clinical inflammation increased. Differential miR expression was not detected in HEp-2 or HCjE epithelial cells 48 h post infection with Ct in vitro. HCjE cells, a conjunctival epithelial cell line, had a markedly different miR background expression compared to HEp-2 cells. CONCLUSIONS: In follicular trachoma, expression of miR-155 and miR-184 is correlated with the severity of inflammation. This likely reflects host regulation of the immune response and a prolonged period of wound healing following the clearance of Ct. Prolonged healing may be associated with subsequent development of scarring trachoma.

Trachoma and Ocular Chlamydial Infection in the Era of Genomics.

Trachoma is a blinding disease usually caused by infection with Chlamydia trachomatis (Ct) serovars A, B, and C in the upper tarsal conjunctiva. Individuals in endemic regions are repeatedly infected with Ct throughout childhood. A proportion of individuals experience prolonged or severe inflammatory episodes that are known to be significant risk factors for ocular scarring in later life. Continued scarring often leads to trichiasis and in-turning of the eyelashes, which causes pain and can eventually cause blindness. The mechanisms driving the chronic immunopathology in the conjunctiva, which largely progresses in the absence of detectable Ct infection in adults, are likely to be multifactorial. Socioeconomic status, education, and behavior have been identified as contributing to the risk of scarring and inflammation. We focus on the contribution of host and pathogen genetic variation, bacterial ecology of the conjunctiva, and host epigenetic imprinting including small RNA regulation by both host and pathogen in the development of ocular pathology. Each of these factors or processes contributes to pathogenic outcomes in other inflammatory diseases and we outline their potential role in trachoma.

Plasmid copy number and disease severity in naturally occurring ocular Chlamydia trachomatis infection.

The Chlamydia trachomatis plasmid is a virulence factor. Plasmid copy number, C. trachomatis load and disease severity were assessed in a treatment-naive population where trachoma is hyperendemic. By using droplet digital PCR, plasmid copy number was found to be stable (median, 5.34 [range, 1 to 18]) and there were no associations with C. trachomatis load or disease severity.

Innovations in Practice: Feasibility of the development and well-being assessment as an adjunct to clinical assessment in child and adolescent mental health services.

BACKGROUND: Child and Adolescent Mental Health services (CAMHS) might benefit from the use of structured diagnostic assessments as an adjunct to clinical assessment. Such assessments will only support clinical practice if their completion avoids too great a burden to parents and services, and if the resulting information is useful to practitioners. METHOD: Parents were asked to complete the Development And Well-Being Assessment (DAWBA) before their initial appointment at a community CAMHS, and DAWBAs were disclosed to the assessing practitioners in a random half of cases. Parents and Practitioners were asked to complete a questionnaire about their experience of the DAWBA. Parents completed the experience of services questionnaire 6 months after the baseline. RESULTS: Most parents found the interview easy to understand. Many reported that the experience of completing the interview changed the way that they thought about their child's difficulties in a positive manner. Practitioner reports were also mainly positive. The mean helpfulness score adjusted for the clustering of cases within practitioners out of 1-5 for very unhelpful to very helpful was 4.04 (95% Confidence Interval: 3.89-4.18). There was no association between practitioner access to the DAWBA and parent reported satisfaction on the Experiences of Services Questionnaire (mean difference 0.74, 95% confidence interval -0.59-02.06, p0.27). CONCLUSIONS: With the right supporting arrangements in place, the DAWBA would be a feasible assessment tool in community CAMHS.

Field- and laboratory-based studies on correlates of Chlamydia trachomatis transmission by Musca sorbens: Determinants of fly-eye contact and investigations into fly carriage of elementary bodies.

Musca sorbens (Diptera: Muscidae) flies are thought to be vectors of the blinding eye disease trachoma, carrying the bacterium Chlamydia trachomatis (Ct) between the eyes of individuals. While their role as vectors has been convincingly demonstrated via randomised controlled trials in The Gambia, studies of fly-borne trachoma transmission remain scant and as such our understanding of their ability to transmit Ct remains poor. We examined fly-eye contact and caught eye-seeking flies from 494 individuals (79% aged ≤9 years) in Oromia, Ethiopia. Ct-carrying flies (harbouring Ct DNA) were found to cluster spatially in and nearby to households in which at least one resident had Ct infection. Fly-eye contact was positively associated with the presence of trachoma (disease), lower human body weight and increased human body temperature. Studies of laboratory-reared M. sorbens indicated that Ct is found both externally and internally following feeds to Ct culture, with scanning electron microscopy revealing how Ct bodies can cling to fly hairs (setae). Testing for Ct on field-caught M. sorbens found fly 'bodies' (thorax, wings and abdomen) to consistently test positive for Ct while legs and heads were infrequently Ct-positive. These studies strongly support the role of M. sorbens as vectors of trachoma and highlight the need for improved understanding of fly-borne trachoma transmission dynamics and vector competence.

Genomic surveillance of Anopheles mosquitoes on the Bijagós Archipelago using custom targeted amplicon sequencing identifies mutations associated with insecticide resistance.

BACKGROUND: Insecticide resistance is reducing the efficacy of vector control interventions, consequently threatening efforts to control vector-borne diseases, including malaria. Investigating the prevalence of molecular markers of resistance is a useful tool for monitoring the spread of insecticide resistance in disease vectors. The Bijagós Archipelago (Bijagós) in Guinea-Bissau is a region of stable malaria transmission where insecticide-treated nets are the mainstay for malaria control. However, the prevalence of molecular markers of insecticide resistance in malaria vectors is not well understood. METHODS: A total of 214 Anopheles mosquitoes were analysed from 13 islands across the Bijagós. These mosquitoes were collected using CDC light traps in November 2019, during the peak malaria transmission season. High-throughput multiplex amplicon sequencing was used to investigate the prevalence of 17 different molecular markers associated with insecticide resistance in four genes: vgsc, rdl, ace1 and gste2. RESULTS: Of the 17 screened mutations, four were identified in mosquitoes from the Bijagós: vgsc L995F (12.2%), N1570Y (6.2%) and A1746S (0.7%) and rdl A269G (1.1%). This study is the first to report the L995F knock-down resistance (kdr)-west allele in Anopheles melas on the Archipelago. An additional eight non-synonymous single-nucleotide polymorphisms were identified across the four genes which have not been described previously. The prevalences of the vgsc L995F and N1570Y mutations were higher on Bubaque Island than on the other islands in this study; Bubaque is the most populous island in the archipelago, with the greatest population mobility and connection to continental Guinea-Bissau. CONCLUSIONS: This study provides the first surveillance data for genetic markers present in malaria vectors from islands across the Bijagós Archipelago. Overall prevalence of insecticide resistance mutations was found to be low. However, the identification of the vgsc L995F and N1570Y mutations associated with pyrethroid resistance warrants further monitoring. This is particularly important as the mainstay of malaria control on the islands is the use of pyrethroid insecticide-treated nets.

Development and evaluation of a next-generation digital PCR diagnostic assay for ocular Chlamydia trachomatis infections.

Droplet digital PCR (ddPCR) is an emulsion PCR process that performs absolute quantitation of nucleic acids. We developed a ddPCR assay for Chlamydia trachomatis infections and found it to be accurate and precise. Using PCR mixtures containing plasmids engineered to include the PCR target sequences, we were able to quantify with a dynamic range between 0.07 and 3,160 targets/µl (r(2) = 0.9927) with >95% confidence. Using 1,509 clinical conjunctival swab samples from a population in which trachoma is endemic in Guinea Bissau, we evaluated the specificity and sensitivity of the quantitative ddPCR assay in diagnosing ocular C. trachomatis infections by comparing the performances of ddPCR and the Roche Amplicor CT/NG test. We defined ddPCR tests as positive when we had ≥95% confidence in a nonzero estimate of target load. The sensitivity of ddPCR against Amplicor was 73.3% (95% confidence interval [CI], 67.9 to 78.7%), and specificity was 99.1% (95% CI, 98.6 to 99.6%). Negative and positive predictive values were 94.6% (95% CI, 93.4 to 95.8%) and 94.5% (95% CI, 91.3 to 97.7%), respectively. Based on Amplicor CT/NG testing, the estimated population prevalence of C. trachomatis ocular infection was ∼17.5%. Receiver-operator curve analysis was used to select critical cutoff values for use in clinical settings in which a balance between higher sensitivity and specificity is required. We concluded that ddPCR is an effective diagnostic technology suitable for both research and clinical use in diagnosing ocular C. trachomatis infections.

Can standardized diagnostic assessment be a useful adjunct to clinical assessment in child mental health services? A randomized controlled trial of disclosure of the Development and Well-Being Assessment to practitioners.

PURPOSE: While research demands standardized diagnostic assessments as an indication of sufficient methodological rigour, there is debate about their application to clinical practice. The Development and Well-Being Assessment (DAWBA) provides a structured assessment of psychiatric disorder. Since it can be completed on-line, it could be used by Child and Adolescent Mental Health Services with few additional demands on staff. Access to the standardized diagnostic information as an adjunct to clinical assessment could reduce the number of appointments spent on assessment, free up practitioner time to work on engagement and improve clinical outcomes by increasing the accuracy of assessment and thus access to the appropriate evidence-based treatment. METHOD: Randomized controlled trial of the disclosure of the DAWBA to the assessing practitioner (n = 117) versus assessment at normal (n = 118) and analysed by "intention to disclose". RESULTS: Exposure to the DAWBA may increase agreement between the DAWBA and practitioners about some anxiety disorders, but detected no other statistically significant increased agreement for other disorders, nor a reduced need for further assessment, the number of difficulties recognised or influence on outcomes. CONCLUSIONS: The results may be explained by the inadequacy of the DAWBA, lack of statistical power to detect any effects that were present or a reluctance of some practitioners to use the DAWBA in their assessment. Future research might benefit from exploring the use of the DAWBA or similar assessments as a referral rather than an assessment tool, and exploring how practitioners and parents experience and use the DAWBA and what training might optimise the utility of the DAWBA to clinical practice.

Validation of a method for the dry preservation and rehydration of Anopheles gambiae sensu lato for parity analysis to assess the impact of vector control measures in the field.

BACKGROUND: As the control of malaria remains heavily dependent on vector management interventions, it is important to understand the impact of these on mosquito populations. Age-grading is a valuable tool for this; however, logistical challenges in remote, resource-poor areas make current methodologies difficult to incorporate into clinical trials and routine surveillance. Our aim was to validate a methodology that could be easily implemented in such settings. Using dried mosquito specimens instead of freshly killed ones, we validated the commonly used ovarian tracheation technique for assessing population age structure. METHODS: Laboratory-reared Anopheles coluzzii mosquitoes with known parity status were dry preserved in silica gel for up to 12 weeks and rehydrated prior to parity assessment. The results were compared to parity results for freshly killed mosquitoes from the same colony. Preserved, field-caught Anopheles gambiae sensu lato (s.l.) from Guinea-Bissau were assessed by three different assessors blinded to each other's scores. An overall index of agreement was calculated using inter-rater reliability of all assessor pairings. The impact of preservation time was investigated using a one-way ANOVA to look for differences in assessor agreement over three time periods. RESULTS: The parity status was correctly identified for 90% of dry preserved and rehydrated insectary-reared An. coluzzii and for 98% of freshly killed insectary-reared An. coluzzii. The inter-rater reliability was highest (0.94) for freshly killed An. coluzzii. The results for all time points showed excellent strength of agreement between assessors. For field-caught An. gambiae s.l., the overall index of agreement between all three assessors was 0.86 (95% confidence interval 0.78-0.93), indicating almost perfect agreement. There was no significant difference between assessor agreement between time frames. CONCLUSIONS: Dry preserving and rehydrating Anopheles mosquitoes provides an alternative to using freshly killed mosquitoes to assess the efficacy of a control intervention in remote settings where it is logistically difficult to dissect fresh specimens. This method also provides the flexibility required for parity assessment to be done on larger scales over bigger areas.

Population dynamics and drug resistance mutations in Plasmodium falciparum on the Bijagós Archipelago, Guinea-Bissau.

Following integrated malaria control interventions, malaria burden on the Bijagós Archipelago has significantly decreased. Understanding the genomic diversity of circulating Plasmodium falciparum malaria parasites can assist infection control, through identifying drug resistance mutations and characterising the complexity of population structure. This study presents the first whole genome sequence data for P. falciparum isolates from the Bijagós Archipelago. Amplified DNA from P. falciparum isolates sourced from dried blood spot samples of 15 asymptomatic malaria cases were sequenced. Using 1.3 million SNPs characterised across 795 African P. falciparum isolates, population structure analyses revealed that isolates from the archipelago cluster with samples from mainland West Africa and appear closely related to mainland populations; without forming a separate phylogenetic cluster. This study characterises SNPs associated with antimalarial drug resistance on the archipelago. We observed fixation of the PfDHFR mutations N51I and S108N, associated with resistance to sulphadoxine-pyrimethamine, and the continued presence of PfCRT K76T, associated with chloroquine resistance. These data have relevance for infection control and drug resistance surveillance; particularly considering expected increases in antimalarial drug use following updated WHO recommendations, and the recent implementation of seasonal malaria chemoprevention and mass drug administration in the region.

Trachoma risk factors in Oromia Region, Ethiopia.

BACKGROUND: Trachoma, the leading infectious cause of blindness, is caused by the bacterium Chlamydia trachomatis (Ct). Despite enormous disease control efforts and encouraging progress, trachoma remains a significant public health problem in 44 countries. Ethiopia has the greatest burden of trachoma worldwide, however, robust data exploring transmission risk factors and the association between socio-economic status is lacking from some regions. This is the first study to investigate these factors in this South-Eastern region of Oromia, Ethiopia. METHODOLOGY/PRINCIPAL FINDINGS: A total of 1211 individuals were enrolled from 247 households in Shashemene Rural district in Oromia Region between 11th April and 25th June 2018, of whom 628 (51.9%) were female and 526 (43.4%) were children aged 1-9 years. Three standardised ophthalmic nurses examined each participant for the presence of active trachoma using the WHO simplified trachoma grading system. Conjunctival swab samples were collected from the upper tarsal conjunctiva of the left eye of each participant. Ct was detected using quantitative PCR. Risk factor data were collected through structured interviews and direct observations. Clinical signs of trachomatous inflammation-follicular among children aged 1-9 (TF1-9) were observed in at least one eye of 106/526 (20.2%) and trachomatous inflammation-intense among children aged 1-9 (TI1-9) were observed in at least one eye of 10/526 (1.9%). We detected Ct by PCR in 23 individuals, of whom 18 (78.3%) were in children aged 1-9 years. Among the 106 children aged 1-9 years with TF, 12 (11.3%) were Ct PCR positive and among 20 children aged 1-9 years with TI, 4 (20.0%) were Ct PCR positive. In a multivariable model, adjusting for household clustering, active trachoma was associated with younger age, the poorest households (aOR = 2.56, 95% CI 1.21-5.51), presence of flies on the face (aOR = 2.87, 95% CI 1.69-6.46), and ocular discharge (aOR = 1.89, 95% CI 1.03-3.24). Pre-school children face washing more than once a day had lower odds of having active trachoma (aOR = 0.59, 95% CI 0.19-0.84). The same was true for washing children's clothing at least once per week (aOR = 0.27, 95% CI 0.33-1.02). CONCLUSION/SIGNIFICANCE: Younger age, personal hygiene in this age group (presence of ocular and nasal discharges, infrequent washing of faces and clothing) and fly-eye contacts are potential risk factors for trachoma in this setting, suggesting that hygiene interventions and environmental improvements are required to suppress transmission to ensure sustained reduction in disease burden Further studies are needed to evaluate these interventions for trachoma control and elimination. Trachoma remains a disease associated with lower socio-economic status, emphasising the need for continued implementation of control measures in addition to poverty reduction interventions in this region.

Protocol for a cluster randomised placebo-controlled trial of adjunctive ivermectin mass drug administration for malaria control on the Bijagós Archipelago of Guinea-Bissau: the MATAMAL trial.

INTRODUCTION: As malaria declines, innovative tools are required to further reduce transmission and achieve elimination. Mass drug administration (MDA) of artemisinin-based combination therapy (ACT) is capable of reducing malaria transmission where coverage of control interventions is already high, though the impact is short-lived. Combining ACT with ivermectin, an oral endectocide shown to reduce vector survival, may increase its impact, while also treating ivermectin-sensitive co-endemic diseases and minimising the potential impact of ACT resistance in this context. METHODS AND ANALYSIS: MATAMAL is a cluster-randomised placebo-controlled trial. The trial is being conducted in 24 clusters on the Bijagós Archipelago, Guinea-Bissau, where the peak prevalence of Plasmodium falciparum (Pf) parasitaemia is approximately 15%. Clusters have been randomly allocated to receive MDA with dihydroartemisinin-piperaquine and either ivermectin or placebo. The primary objective is to determine whether the addition of ivermectin MDA is more effective than dihydroartemisinin-piperaquine MDA alone in reducing the prevalence of P. falciparum parasitaemia, measured during peak transmission season after 2 years of seasonal MDA. Secondary objectives include assessing prevalence after 1 year of MDA; malaria incidence monitored through active and passive surveillance; age-adjusted prevalence of serological markers indicating exposure to P. falciparum and anopheline mosquitoes; vector parous rates, species composition, population density and sporozoite rates; prevalence of vector pyrethroid resistance; prevalence of artemisinin resistance in P. falciparum using genomic markers; ivermectin's impact on co-endemic diseases; coverage estimates; and the safety of combined MDA. ETHICS AND DISSEMINATION: The trial has been approved by the London School of Hygiene and Tropical Medicine's Ethics Committee (UK) (19156) and the Comite Nacional de Eticas de Saude (Guinea-Bissau) (084/CNES/INASA/2020). Results will be disseminated in peer-reviewed publications and in discussion with the Bissau-Guinean Ministry of Public Health and participating communities. TRIAL REGISTRATION NUMBER: NCT04844905.

A practical critique of antifungal treatment guidelines for haemato-oncologists.

The management of invasive fungal disease (IFD) in the haemato-oncology setting remains a challenge. This article reviews recent guidelines relating to IFD for their similarities and differences, as well as applying the Appraisal of Guidelines Research and Evaluation (AGREE) criteria. The guidelines' recommendations on antifungal prophylaxis, empirical and definitive treatment of candidiasis and aspergillosis are summarized; also, minimum standards for diagnosis and follow-up are discussed. This critique of the reviewed guidelines is a practical guide to physicians and commissioners in making local policies for IFD management.