High Levels Of Co-infection Research Articles

Tick-borne pathogens and body condition of cattle in smallholder rural livestock production systems in East and West Africa

BackgroundThe majority of the African population lives in rural areas where they heavily depend on crop and livestock production for their livelihoods. Given their socio-economic importance, we initiated a standardized multi-country (Benin, Burkina Faso, Ghana, Nigeria, Ethiopia Tanzania and Uganda) surveillance study to assess the current status of important tick-borne haemoparasites (TBHPs) of cattle.MethodsWe assessed pathogen prevalences (Anaplasma marginale, Anaplasma centrale, Babesia bigemina, Babesia bovis, Ehrlichia ruminantium, and Theileria parva) in the blood of 6447 animals spread over fourteen districts (two districts per country). In addition, we screened for intrinsic (sex, weight, body condition) and extrinsic (husbandry, tick exposure) risk factors as predictors of infections with TBHPs.ResultsThere was a large macro-geographic variation observed in A. marginale, B. bigemina, B. bovis and E. ruminantium prevalences. Most correlated with the co-occurrence of their specific sets of vector-competent ticks. Highest numbers of infected cattle were found in Ghana and Benin, and lowest in Burkina Faso. While T. parva was seldomly found (Uganda only: 3.0%), A. marginale was found in each country with a prevalence of at least 40%. Babesia bovis infected individuals had lower body condition scores. Age (as estimated via body weight) was higher in A. marginale infected cattle, but was negatively correlated with B. bigemina and E. ruminantium prevalences. Ehrlichia ruminantium infection was more often found in males, and A. marginale more often in transhumance farming. High levels of co-infection, especially the combination A. marginale × B. bigemina, were observed in all countries, except for Uganda and Burkina Faso. Babesia bigemina was more or less often observed than expected by chance, when cattle were also co-infected with E. ruminantium or A. marginale, respectively.ConclusionsTick-borne pathogens of cattle are ubiquitous in African’s smallholder cattle production systems. Our standardized study will help a wide range of stakeholders to provide recommendations for TBHP surveillance and prevention in cattle, especially for B. bovis which heavily impacts production and continues its spread over the African continent via the invasive Rhipicephalus microplus tick.Graphical

Ending the HIV Epidemic: Contributions Resulting From Syphilis Partner Services.

There is a high level of coinfection with human immunodeficiency virus (HIV) among persons diagnosed with syphilis in the United States. Public health workers at state and local health departments help inform exposed partners to sexually transmitted disease (STD)/HIV infections to facilitate early testing and treatment (partner services). The federal initiative, Ending the HIV Epidemic (EHE), identifies 4 key strategies: diagnose, treat, prevent, and respond. This study describes the contributions of syphilis partner services to the EHE strategies in a county prioritized by the EHE plan. A retrospective record review of reported early syphilis cases (less than 1 year's duration) between 2016 and 2018 in the Indianapolis area was conducted to determine the extent of new HIV diagnoses, retention in HIV care, and other evidence-based HIV prevention interventions occurring after provision of syphilis partner services. A total of 752 partners to early syphilis were attempted to be notified of exposure. There were 1,457 case patients and partners that received STD/HIV prevention counseling; 400 partners received STD treatment, 352 partners learned their HIV status, and 22 received new HIV diagnoses, with 68% retained in medical care and 60% virally suppressed. Two thirds of partner services were completed within 21 days. New HIV positivity among partners to HIV-negative syphilis case patients was 3.5% and 14% among HIV-positive syphilis case patients. Partner services for syphilis was an effective method of addressing the EHE strategies, resulting in persons at risk tested, STD treatment provided, behavioral prevention counseling provided, and new HIV cases identified, leading to retention in medical care and viral suppression.

Molecular assessment of Bartonella in Gerbillus nanus from Saudi Arabia reveals high levels of prevalence, diversity and co-infection

Bartonellae bacteria are associated with several re-emerging human diseases. These vector-borne pathogens have a global distribution, yet data on Bartonella prevalence and diversity in the Arabian Peninsula are limited. In this study we assessed the Bartonella infection status of the Baluchistan gerbil (Gerbillus nanus), a species associated with pastoral communities throughout the Middle East region, using a multi-gene PCR screening approach. The results demonstrated that 94 (68.1%) of the 138 gerbils trapped on a monthly basis, over a period of one year, were PCR-positive. Sequencing of the gltA gene region confirmed the presence of four discrete Bartonella lineages (I–IV) and high levels of co-infection (33.0%). Each of the four lineages, varied in overall abundance (7.5%–47.9%) and had discernible seasonal peaks. Bartonella status was significantly correlated with ectoparasite presence, but not with sex, nor with season. Statistical analyses further revealed that co-infected individuals had a significantly higher relative body condition. Multi-locus sequence analysis (MLSA) performed with a concatenated dataset of three genetic loci (gltA, nuoG, and rpoB), 1452 nucleotides (nt) in length confirmed that lineage IV, which occurred in 24 PCR-positive animals (25.5%), is most closely related to zoonotic B. elizabethae. The remaining three lineages (I-III) formed a monophyletic clade which, on the basis of gltA was shown to contain bartonellae from diverse Gerbillinae species from the Middle East, suggestive of a gerbil-associated species complex in this region. Lineage I was identical to a Candidatus B. sanaae strain identified previously in Bushy-tailed jirds (Sekeetamys calurus) from Egypt, wherease MLSA indicate that lineages II and III are novel. The high levels of infection and co-infection, together with the presence of multiple Bartonella lineages indicate that Gerbillus nanus is likely a natural reservoir of Bartonella in the Arabian Peninsula.

Canine vector-borne pathogens in semi-domesticated dogs residing in northern Cambodia.

BackgroundIn Southeast Asia, the canine vector-borne pathogens Babesia spp., Ehrlichia canis, Anaplasma platys, Hepatozoon canis, haemotropic mycoplasmas and Dirofilaria immitis cause significant morbidity and mortality in dogs. Moreover, dogs have also been implicated as natural reservoirs for Rickettsia felis, the agent of flea-borne spotted fever, increasingly implicated as a cause of undifferentiated fever in humans in Southeast Asia. The objective of this study was to determine the prevalence and diversity of canine vector-borne pathogens in 101 semi-domesticated dogs from rural Cambodia using molecular diagnostic techniques.ResultsThe most common canine vector-borne pathogens found infecting dogs in this study were Babesia vogeli (32.7 %) followed by Ehrlichia canis (21.8 %), Dirofilaria immitis (15.8 %), Hepatozoon canis (10.9 %), Mycoplasma haemocanis (9.9 %) and “Candidatus Mycoplasma haematoparvum” (2.9 %). A high level of co-infection with CVBD agents (23.8 %) was present, most commonly B. vogeli and E. canis. Naturally occurring R. felis infection was also detected in 10.9 % of dogs in support of their role as a natural mammalian reservoir for flea-borne spotted fever in humans.ConclusionsThis study reports for the first time, the prevalence and diversity of CVBD pathogens in dogs in Cambodia. In total, five species of CVBD pathogens were found infecting semi-domesticated dogs and many were co-infected with two or more pathogens. This study supports the role of dogs as natural mammalian reservoirs for R. felis, the agent of flea-borne spotted fever in humans.

Prevalence and phylogenetic analysis of haemoplasmas from cats infected with multiple species

Mycoplasma haemofelis (Mhf), ‘Candidatus Mycoplasma haemominutum’ (CMhm) and ‘Candidatus Mycoplasma turicensis’ (CMt) are agents of feline haemoplasmosis and can induce anaemia in cats. This study aimed to determine the prevalence and phylogeny of haemoplasma species in cats from Brazil's capital and surrounding areas, and whether correlation with haematological abnormalities existed. Feline haemoplasmas were found in 13.8% of 432 cats. CMhm was the most prevalent species (in 13.8% of cats), followed by Mhf (11.1%) and CMt (4.4%). Over 80% of haemoplasma-infected cats harboured two or more feline haemoplasma species: 7.1% of cats were co-infected with Mhf/CMhm, 0.4% with CMhm/CMt and 3.9% with Mhf/CMhm/CMt. Male gender was significantly associated with haemoplasma infections. No association was found between qPCR haemoplasma status and haematological variables, however CMhm relative copy numbers were correlated with red blood cell (RBC) numbers and packed cell volume (PCV). Haemoplasma 16S rRNA gene sequences (>1Kb) were derived from co-infected cats using novel haemoplasma species-specific primers. This allowed 16S rRNA gene sequences to be obtained despite the high level of co-infection, which precluded the use of universal 16S rRNA gene primers. Within each species, the Mhf, CMhm and CMt sequences showed >99.8%, >98.5% and >98.8% identity, respectively. The Mhf, CMhm and CMt sequences showed >99.2%, >98.4% and >97.8% identity, respectively, with GenBank sequences. Phylogenetic analysis showed all Mhf sequences to reside in a single clade, whereas the CMhm and CMt sequences each grouped into three distinct subclades. These phylogeny findings suggest the existence of different CMhm and CMt strains.

Global burden, distribution, and interventions for infectious diseases of poverty

Infectious diseases of poverty (IDoP) disproportionately affect the poorest population in the world and contribute to a cycle of poverty as a result of decreased productivity ensuing from long-term illness, disability, and social stigma. In 2010, the global deaths from HIV/AIDS have increased to 1.5 million and malaria mortality rose to 1.17 million. Mortality from neglected tropical diseases rose to 152,000, while tuberculosis killed 1.2 million people that same year. Substantial regional variations exist in the distribution of these diseases as they are primarily concentrated in rural areas of Sub-Saharan Africa, Asia, and Latin America, with geographic overlap and high levels of co-infection. Evidence-based interventions exist to prevent and control these diseases, however, the coverage still remains low with an emerging challenge of antimicrobial resistance. Therefore, community-based delivery platforms are increasingly being advocated to ensure sustainability and combat co-infections.Because of the high morbidity and mortality burden of these diseases, especially in resource-poor settings, it is imperative to conduct a systematic review to identify strategies to prevent and control these diseases. Therefore, we attempted to evaluate the effectiveness of one of these strategies, that is community-based delivery for the prevention and treatment of IDoP. In this paper, we describe the burden, epidemiology, and potential interventions for IDoP. In subsequent papers of this series, we describe the analytical framework and the methodology used to guide the systematic reviews, and report the findings and interpretations of our analyses of the impact of community-based strategies on individual IDoPs.

Disease resistance in Atlantic salmon (Salmo salar): coinfection of the intracellular bacterial pathogen Piscirickettsia salmonis and the sea louse Caligus rogercresseyi.

BackgroundNaturally occurring coinfections of pathogens have been reported in salmonids, but their consequences on disease resistance are unclear. We hypothesized that 1) coinfection of Caligus rogercresseyi reduces the resistance of Atlantic salmon to Piscirickettsia salmonis; and 2) coinfection resistance is a heritable trait that does not correlate with resistance to a single infection.MethodologyIn total, 1,634 pedigreed Atlantic salmon were exposed to a single infection (SI) of P. salmonis (primary pathogen) or coinfection with C. rogercresseyi (secondary pathogen). Low and high level of coinfection were evaluated (LC = 44 copepodites per fish; HC = 88 copepodites per fish). Survival and quantitative genetic analyses were performed to determine the resistance to the single infection and coinfections.Main Findings C. rogercresseyi significantly increased the mortality in fish infected with P. salmonis (SI mortality = 251/545; LC mortality = 544/544 and HC mortality = 545/545). Heritability estimates for resistance to P. salmonis were similar and of medium magnitude in all treatments (h 2 SI = 0.23±0.07; h 2 LC = 0.17±0.08; h 2 HC = 0.24±0.07). A large and significant genetic correlation with regard to resistance was observed between coinfection treatments (rg LC-HC = 0.99±0.01) but not between the single and coinfection treatments (rg SI-LC = −0.14±0.33; rg SI-HC = 0.32±0.34).Conclusions/Significance C. rogercresseyi, as a secondary pathogen, reduces the resistance of Atlantic salmon to the pathogen P. salmonis. Resistance to coinfection of Piscirickettsia salmonis and Caligus rogercresseyi in Atlantic salmon is a heritable trait. The absence of a genetic correlation between resistance to a single infection and resistance to coinfection indicates that different genes control these processes. Coinfection of different pathogens and resistance to coinfection needs to be considered in future research on salmon farming, selective breeding and conservation.

Zoonotic bacterial survey assessed by next-generation sequencing

Rodents represent one of the major sources of pathogens; most of them are vectored by ticks. Tick-borne diseases are very diverse and cause a wide range of diseases in livestock and human populations. Rodents, carrying ticks, are distributed across a vast range of natural habitats and they often live in close contact with humans and their domestic animals, exposing them to zoonoses circulating in natural ecosystems. In this study, we analyse the potential of Next-Generation Sequencing (NGS) technologies as a tool for large-scale survey of bacterial zoonotic pathogens carried by rodents. We combined two NGS approaches in order to establish a list of zoonotic bacteria and to identify their distribution in individuals of rodents in natural populations. Briefly, RNA/DNA were extracted from the spleen of 192 rodents collected in Northeast France. RNA from all samples was pooled and submitted to high throughput RNA sequencing (RNAseq). Succeeding de novo assembly, bacterial contigs were assigned to the closest already-known taxa, revealing a list of zoonotic bacteria for the whole sample. Parallel, DNA samples were submitted to meta-barcoding approach: each sample was amplified by PCR using universal primers tagged at the V4 region of the 16S rRNA. The amplified templates were multiplexed and submitted to 454-pyrosequencing. The resulting dataset was demultiplexed using a home-made pipeline that assigns each read to a sample using the tagged primers, following these were processed using Mothur pipeline to construct OTUs and classify them using the RDP database. These methods allowed listing bacteria detected in each rodent and, so derive the prevalence, coinfections and bacteria interactions. DNA/RNA of the following bacteria genera were detected by both approaches, RNAseq and DNA 16S-metabarcoding: Bartonella, Leptospira, Borrelia, Rickettsia, Treponema, Neisseria, Spiroplasma, Klebsiella, Listeria and Shigella. Some unexpected genera were detected; such as Orientia, up to now only found in Asia or Helicobacter, generally thought to be restricted to animal guts. Several bacterial pathogens explored by RNAseq passed undetected by 16S-metabarcoding: Anaplasma, (Neo)Ehrlichia, Wolbachia, Brucella, Coxiella, Campylobacter, Mycoplasma, Salmonella, Yersinia, and Francisella. Furthermore, 16S meta-barcoding allowed to specify prevalence of bacteria within our sample, and revealed high level of coinfection in wild rodents. Our data demonstrate that NGS allows having a rather complete screening of pathogenic bacteria present in animal reservoirs without any a priori on their presence, while having a price compatible with cohort studies. NGS approaches are becoming the new routine approaches in large-scale epidemiological studies.

A Pilot Study Assessing the Impact of a Fortified Supplementary Food on the Health and Well-Being of Crèche Children and Adult TB Patients in South Africa

The South African population faces many of the global concerns relating to micronutrient deficiency and the impact this has on health and well-being. Moreover, there is a high prevalence of HIV infection, compounded by a high level of co-infection with TB.This pilot study evaluates the impact of a fortified supplementary food on the health and well-being of a cohort of crèche children, aged 3 to 6, and adult TB patients drawn from the Presidential Node of Alexandra, Johannesburg, South Africa. A further aim of this study was to evaluate the sensitivity and validity of non-invasive indicators of nutritional status in a field-based population sample.The investigational product, e’Pap, is supported by extensive anecdotal evidence that whole grain cereals with food-style nutrients constitute an effective supplementary food for those suffering from the effects of food insecurity, poor health and well-being, and coping with TB and HIV infection.The results indicate a beneficial effect of e’Pap for both study populations, and particularly for adult TB patients, whose baseline data reflected severe food insecurity and malnutrition in the majority of cases. There is evidence to suggest statistically significant improvements in key micronutrient levels, well-being and energy, hand-grip strength, the Bioelectrical Impedance Analysis (BIA) Illness Marker, and certain clinical indicators. Although Body Mass Index (BMI) and Mid Upper Arm Circumference (MUAC) are frequently used as standard measures to evaluate the efficacy of nutritional interventions, these indicators were not sufficiently sensitive in this study. Nor does weight gain necessarily indicate improved nutritional status. Hand-grip strength, lean body mass, and the BIA Illness Marker seem to be more useful indicators of change in nutritional status.

Amoebic gill disease (AGD) in Atlantic salmon ( Salmo salar) farmed in Chile

Between May and November 2007, three marine Atlantic salmon farms around Chiloé Island, Chile, reported mortalities in which affected fish presented with Caligus rogercresseyi infections and gross gill lesions characteristic of amoebic gill disease (AGD). Histological examination of the gills from affected fish confirmed the presence of AGD lesions. Trophozoites possessing one or more endosymbiotic Perkinsela amoeba-like organisms (PLOs) were observed in association with hyperplastic tissue. Further analyses were undertaken using a combination of PCR and in situ hybridization and the trophozoites were identified as Neoparamoeba perurans. Thus, our data indicate that N. perurans is a causal agent of AGD in Chile. However, it is possible that AGD was not the single cause of mortalities in the epizootics investigated here. The exceptionally high level of co-infection with Caligus rogercresseyi (maximum mean intensity 34, prevalence 100%), could have contributed to the production losses.

Genetic Diversity Among Viruses Associated with Sugarcane Mosaic Disease in Tucumán, Argentina

Sugarcane leaves with mosaic symptoms were collected in 2006--07 in Tucumán (Argentina) and analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR) restriction fragment length polymorphism (RFLP) and sequencing of a fragment of the Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) coat protein (CP) genes. SCMV was detected in 96.6% of samples, with 41% showing the RFLP profile consistent with strain E. The remaining samples produced eight different profiles that did not match other known strains. SCMV distribution seemed to be more related to sugarcane genotype than to geographical origin, and sequence analyses of CP genes showed a greater genetic diversity compared with other studies. SrMV was detected in 63.2% of samples and most of these were also infected by SCMV, indicating that, unlike other countries and other Argentinean provinces, where high levels of co-infection are infrequent, co-existence is common in Tucumán. RFLP analysis showed the presence of SrMV strains M (68%) and I (14%), while co-infection between M and H strains was present in 18% of samples. Other SCMV subgroup members and the Sugarcane streak mosaic virus (SCSMV) were not detected. Our results also showed that sequencing is currently the only reliable method to assess SCMV and SrMV genetic diversity, because RT-PCR-RFLP may not be sufficiently discriminating.

Survival following HIV infection of a cohort followed up from seroconversion in the UK

To estimate changes over calendar time in survival following HIV seroconversion in the era of HAART and to provide updated survival estimates. Using data from a UK cohort of persons with well estimated dates of HIV seroconversion, we analysed time from seroconversion to death from any cause using Cox models, adjusted for prognostic factors. Kaplan-Meier methods were then used to determine the expected survival in each calendar period. 2275 seroconverters were included with 18 695 person-years of follow up. A total of 444 (20%) died. The relative risk of death, compared with pre-1996, decreased over time to 0.63 [95% confidence interval (CI), 0.48-0.81], 0.24 (0.17-0.34), 0.14 (0.10-0.21), 0.08 (0.05-0.13) and 0.03 (0.02-0.06) in 1996-1997, 1998-1999, 2000-2001, 2002-2003 and 2004-2006, respectively. An elevated risk of death was associated with older age at seroconversion [hazard ratio (HR), 1.49; 95% CI, 1.34-1.66 per 10-year increase] and HIV infection through injecting drug use (HR, 1.53; 95% CI, 1.17-2.00). In 2000-2006, the proportion of individuals expected to survive 5, 10 and 15 years following seroconversion was 99%, 94% and 89%, respectively. Survival following HIV seroconversion has continued to improve over calendar time in our cohort, even in the more recent years of HAART availability. HIV seroconverters, by definition identified early in their infection, are likely to have the greatest opportunity for intervention; if similar high survival expectations are to be seen in the wider HIV-infected population, early diagnosis is likely to be crucial.

Lymphogranuloma Venereum in the United Kingdom

Over the past 2 years, lymphogranuloma venereum (LGV), caused by L serovars of Chlamydia trachomatis, has emerged as a significant problem among men who have sex with men (MSM). We report on, to our knowledge, the largest case series of LGV to date, with detailed epidemiological and clinical characteristics of the epidemic in the United Kingdom. A national diagnostic service and surveillance system was established in October 2004. Cases were confirmed by the presence of C. trachomatis and an LGV serovar (L1, L2, or L3) from genotyping. For confirmed cases, an enhanced surveillance questionnaire was sent to the clinician. Through February 2006, a total of 327 cases of LGV were confirmed. Cases were diagnosed across the United Kingdom, with the majority from London (71%) and Brighton (13%). Case reports were received for 282 MSM. The majority (96%) had proctitis, many with severe local and systemic symptoms. There was a high level of coinfection with human immunodeficiency virus (76%), hepatitis C (19%), and other sexually transmitted infections (39%). Nine cases of human immunodeficiency virus infection were diagnosed around the same time as LGV. Most cases were acquired within the United Kingdom, although patients with early cases were more likely to report contacts in The Netherlands. We found a significant burden of this once-rare sexually transmitted infection among MSM in the United Kingdom. LGV may be contributing to the epidemic of human immunodeficiency virus infection by facilitating transmission. Further control efforts are required, including awareness campaigns, continued detailed surveillance, and expanded chlamydia testing among MSM.

Evolution of Mutational Robustness in an RNA Virus

Mutational (genetic) robustness is phenotypic constancy in the face of mutational changes to the genome. Robustness is critical to the understanding of evolution because phenotypically expressed genetic variation is the fuel of natural selection. Nonetheless, the evidence for adaptive evolution of mutational robustness in biological populations is controversial. Robustness should be selectively favored when mutation rates are high, a common feature of RNA viruses. However, selection for robustness may be relaxed under virus co-infection because complementation between virus genotypes can buffer mutational effects. We therefore hypothesized that selection for genetic robustness in viruses will be weakened with increasing frequency of co-infection. To test this idea, we used populations of RNA phage φ6 that were experimentally evolved at low and high levels of co-infection and subjected lineages of these viruses to mutation accumulation through population bottlenecking. The data demonstrate that viruses evolved under high co-infection show relatively greater mean magnitude and variance in the fitness changes generated by addition of random mutations, confirming our hypothesis that they experience weakened selection for robustness. Our study further suggests that co-infection of host cells may be advantageous to RNA viruses only in the short term. In addition, we observed higher mutation frequencies in the more robust viruses, indicating that evolution of robustness might foster less-accurate genome replication in RNA viruses.

Adaptive Molecular Evolution for 13,000 Phage Generations

Bacteriophage phiX174 was evolved on a continuous supply of sensitive hosts for 180 days ( approximately 13,000 phage generations). The average rate of nucleotide substitution was nearly 0.2% (11 substitutions)/20 days, and, surprisingly, substitutions accumulated in a clock-like manner throughout the study, except for a low rate during the first 20 days. Rates of silent and missense substitutions varied over time and among genes. Approximately 40% of the 71 missense changes and 25% of the 58 silent changes have been observed in previous adaptations; the rate of parallel substitution was highest in the early phase of the evolution, but 7% of the later changes had evolved in previous studies of much shorter duration. Several lines of evidence suggest that most of the changes were adaptive, even many of the silent substitutions. The sustained, high rate of adaptive evolution for 180 days defies a model of adaptation to a constant environment. We instead suggest that continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genomes competing within the same cell.