Antimicrobial resistance in rural settings in Latin America: a scoping review with a One Health lens

Antimicrobial resistance (AMR) in rural Latin America is not fully understood. The transmission pathways are partially known since research predominantly focuses on the urban hospital setting. The contribution to AMR from environmental factors is usually only mentioned in large-scale animal production. To understand the state of the literature on AMR in rural LA, we carried out a scoping review using the One Health (OH) perspective. OH recognises the concomitant contributions and interconnectedness of humans, animal, and the environment, thus, we used the OH perspective to select those articles adopting a holistic view of the problem. We searched original articles in English, Spanish, and Portuguese in four peer-reviewed databases and included 21 publications in the analysis. We charted data on bibliometrics, design, data collection sources, and instruments. We identified the human, animal, and environmental contributions to AMR in rural locations, and information gaps on AMR transmission routes and AMR drivers. Intensive and non-intensive animal production systems and agricultural practices were the most frequently found human contributions to AMR. Poultry, swine, cattle, and fish were the most frequent livestock mentioned as sources of AMR bacteria. Animal carriage and/or transfer of AMR determinants or bacteria was recognised as the primary contribution of livestock to the problem, while water, soil, and farming were predominant environmental contributions. We found that only 1 article out of 21 considered the OH approach as a framework for their sampling scheme, whereas 5 out 21 discussed all the three OH components. There were hardly any descriptions of humans or human waste as reservoirs for AMR in rural locations, and rural health centres or hospitals and wildlife were not represented. No studies identified mining as an anthropogenic activity driving AMR. More OH-oriented studies, with emphasis on molecular approaches-for identification and comparison of AMR genes-are sorely needed to understand better the existence of a network of interconnected transmission routes in rural Latin America and provide efficient strategies to prevent further AMR emergence

Whole-genome characterisation of ESBL-producing E. coli isolated from drinking water and dog faeces from rural Andean households in Peru

E. coli that produce extended-spectrum beta-lactamases (ESBLs) are major multidrug-resistant bacteria. In Peru, only a few reports have characterised the whole genome of ESBL enterobacteria. We aimed to confirm the identity and antimicrobial resistance (AMR) profile of two ESBL isolates from dog faeces and drinking water of rural Andean households and determine serotype, phylogroup, sequence type (ST)/clonal complex (CC), pathogenicity, virulence genes, ESBL genes, and their plasmids. To confirm the identity and AMR profiles, we used the VITEK((R))2 system. Whole-genome sequencing (WGS) and bioinformatics analysis were performed subsequently. Both isolates were identified as E. coli, with serotypes -:H46 and O9:H10, phylogroups E and A, and ST/CC 5259/- and 227/10, respectively. The isolates were ESBL-producing, carbapenem-resistant, and not harbouring carbapenemase-encoding genes. Isolate 1143 ST5259 harboured the astA gene, encoding the EAST1 heat-stable toxin. Both genomes carried ESBL genes (blaEC-15, blaCTX-M-8, and blaCTX-M-55). Nine plasmids were detected, namely IncR, IncFIC(FII), IncI, IncFIB(AP001918), Col(pHAD28), IncFII, IncFII(pHN7A8), IncI1, and IncFIB(AP001918). Finding these potentially pathogenic bacteria is worrisome given their sources and highlights the importance of One-Health research efforts in remote Andean communities

Household-level risk factors for water contamination and antimicrobial resistance in drinking water among households with children under 5 in rural San Marcos, Cajamarca, Peru

Household water contamination at point of use depends on human, animal and environmental factors embodying all aspects of a One Health approach. This study investigated the association between household factors, the presence of thermotolerant coliform, and the presence of antibiotic resistant bacteria in drinking water among 314 households with children under 5 in Cajamarca, Peru. This study analysed data from a baseline sampling of a randomized controlled trial, including household surveys covering household water management and factors such as household animals, as well as microbiological data from samples collected from drinking water. Data were analysed using generalized linear models. Drinking water samples collected from narrow-mouthed containers were less likely to be contaminated than samples collected from the faucet (OR = 0.55, p = 0.030) or wide mouthed containers. The presence of thermotolerant coliform was associated with owning farm birds, which increased the proportion of contamination from 42.2% to 59.1% (OR = 1.98, p = 0.017) and with animal waste observed in the kitchen area, which increased the prevalence of contamination from 51.4% to 65.6% (OR = 1.80, p = 0.024). Resistance to any antibiotic was higher among pig owners at 60%, relative to non-pig owners at 36.4% (OR = 1.97, p = 0.012) as well as households with free-roaming animals in the kitchen area at 59.6% compared to households without free-roaming animals at 39.7% (OR = 2.24, p = 0.035). Recent child antibiotic use increased the prevalence of trimethoprim-sulfamethoxazole resistance among E. coli isolates to 22.3% relative to 16.7% (OR = 3.00, p = 0.037). Overall, these findings suggest that water storage in a secure container to protect from in-home contamination is likely to be important in providing safe drinking water at point of use. In addition, transmission of thermotolerant coliform and AMR between domestic animals and human drinking water supplies is likely. Further research should explore transmission pathways and methods to support safe drinking water access in multi-species households

Gender based water violence: cross cultural evidence of severe harm associated with water insecurity for women and girls

We examined how study participants in Indonesia and Peru viewed the relationship between water insecurity and women's health via thematic analysis of interviews and focus groups. Participants reported that water insecurity led to vaginal infections, miscarriage, premature births, uterine prolapse, poor nutrition, restricted economic opportunities, and intergenerational cycles of poverty. Participants in both countries stated that extreme burdens associated with water insecurity should be categorized as violence. Based on these findings, we developed the concept of “gender-based water violence,” defined as the spectrum of stressors associated with water insecurity that are so severe as to threaten human health and well-being, particularly that of women and girls

Antimicrobial resistance in humans, animals, water and household environs in rural Andean Peru: exploring dissemination pathways through the One Health lens

Antimicrobial resistance (AMR) is a global public health threat, especially for low and middle-income countries (LMIC) where the threat has not been fully identified. Our study aims to describe E. coli AMR in rural communities to expand our knowledge on AMR bacterial contamination. Specifically, we aim to identify and describe potential dissemination routes of AMR-carrying bacteria in humans (children's stools), community water sources (reservoirs and household sources), household environments (yard soil) and domestic animals of subsistence farmers in rural Andean areas. Our cross-sectional study was conducted in rural households in the region of Cajamarca, Peru. A total of 266 samples were collected. Thirty-four point six percent of reservoir water and 45% of household water source samples were positive for thermotolerant coliforms. Of the reservoir water samples, 92.8% were positive for E. coli, and 30.8% displayed resistance to at least one antibiotic, with the highest resistance to tetracycline. E. coli was found in 57.1% of the household water sources, 18.6% of these isolates were multidrug-resistant, and displayed the highest resistance to tetracycline (31.3%). Among samples from the children's drinking water source, 32.5% were positive for thermotolerant coliforms, and 57.1% of them were E. coli. One third of E. coli isolates were multidrug-resistant and displayed the highest AMR to tetracycline (41.6%) and ampicillin (25%). Thermotolerant coliforms were found in all the soil samples, 43.3% of the isolates were positive for E. coli, 34.3% of the E. coli isolates displayed AMR to at least one antibiotic, and displayed the highest AMR to tetracycline (25.7%). We determined thermotolerant coliforms in 97.5% of the child feces samples; 45.3% of them were E. coli, 15.9% displayed multidrug resistance, and displayed the highest resistance to ampicillin (34.1%). We identified thermotolerant coliforms in 67.5% of the animal feces samples. Of those, 38.7% were E. coli, and 37.7% were resistant to at least one antibiotic. For all the samples, the prevalence of resistance to at least one antibiotic in the E. coli and Klebsiella spp. isolates was almost 43% and the prevalence of MDR in the same isolates was nearly 9%, yet the latter nearly doubled (15.9%) in children's stools. Our results provide preliminary evidence for critical pathways and the interconnectedness of animal, human and environmental transmission but molecular analysis is needed to track dissemination routes properly

Prevalence of paramyxoviruses in bats in six areas of Madre de Dios and Puno, Peru with two levels of anthropogenic disturbance

Los Andes tropicales que comprende la región de Madre de Dios, Perú, es considerada una zona de conservación para la biodiversidad; sin embargo, el reciente desarrollo de la zona a través de la pavimentación de la carretera interoceánica (CIO) ha ocasionado un impacto antropogénico en la región. Este estudio tuvo como objetivo identificar la prevalencia de paramixovirus, patógenos emergentes de importancia para la salud pública y animal, en murciélagos capturados a lo largo de los tramos de la CIO sujetos a diferentes grados de perturbación ecológica. La captura se hizo entre octubre de 2009 a octubre de 2010 en tres zonas altamente perturbadas y tres zonas con un grado de perturbación moderado a ligero; además, en la Reserva Nacional de Tambopata como grupo control. Se analizaron muestras de bazo mediante la técnica de RT-PCR semianidado que detecta las regiones conservadas del gen de la polimerasa. Se capturaron 436 murciélagos de 24 géneros y 35 especies, encontrándose una prevalencia de paramixovirus de 10.3% (IC 95%: 7.6-13.6%). La prevalencia fue de 15.7% en lugares clasificados con alto grado de perturbación ecológica, siendo significativamente mayor (p=0.009) que en lugares con moderado grado de perturbación (5.6%) y en la zona control (8.3%). La especie Artibeus planisrostris mostró la más alta frecuencia de infección (37%). Mediante el análisis de secuencia se identificaron tres muestras positivas a paramixovirus agrupadas dentro del género Morbillivirus (no clasificada) en las especies Carollia brevicuda y C. perspicillata; así como miembros del género Rubulavirus (Mapuera virus) en tres muestras de murciélagos adultos de la especie Sturnira lilium colectados en el distrito de Iberia.The tropical Andes, comprising the Madre de Dios region, are a hotspot for biodiversity conservation. Recent development of the area through paving of the interoceanic highway (IOH) resulted in anthropogenic impacts in the region. This study aimed to identify the prevalence of emerging pathogens of public and animal health importance such as Paramyxoviruses among bats trapped along areas of IOH with different ecological impacts. Samples from six study sites along the IOH were collected from October 2009 to October 2010: three highly disturbed areas and three areas with low disturbance. A site located at the Tambopata National Reserve was selected as an undisturbed environment for control. Bat spleens were tested for Paramyxoviruses by nested PCR targeting the conserved motifs of the polymerase gene. A total of 436 bats from 24 different genera were captured, of which 45 (10.32%; CI 95%: 7.6-13.6%) were positive for Paramyxoviruses. The prevalence was higher in areas with more disturbance than in mildly disturbed areas (15.7 vs. 5.6%, p=0.009). The prevalence in the control area was 8.3%. The species Artibeus planirostris showed the highest infection frequency (37%, 17/45). Three positive bats were adults of the Sturnira lilium species collected from one location in Iberia District. Sequence analysis placed these viruses in the Rubulavirus genera (Mapuera virus). The remaining viruses were related to an unclassified Morbillivirus found in bat samples in Brazil during 2013

Seroprevalence and Risk Factors for Rickettsia and Leptospira Infection in Four Ecologically Distinct Regions of Peru.

Rickettsia and Leptospira spp. are under-recognized causes of acute febrile disease worldwide. Rickettsia species are often placed into the spotted fever group rickettsiae (SFGR) and typhus group rickettsiae (TGR). We explored the antibody prevalence among humans for these two groups of rickettsiae in four regions of Peru (Lima, Cusco, Puerto Maldonado, and Tumbes) and for Leptospira spp. in Puerto Maldonado and Tumbes. We also assessed risk factors for seropositivity and collected serum samples and ectoparasites from peri-domestic animals from households in sites with high human seroprevalence. In total, we tested 2,165 human sera for antibodies (IgG) against SFGR and TGR by ELISA and for antibodies against Leptospira by a microscopic agglutination test. Overall, human antibody prevalence across the four sites was 10.6% for SFGR (ranging from 6.2% to 14.0%, highest in Tumbes) and 3.3% for TGR (ranging from 2.6% to 6.4%, highest in Puerto Maldonado). Factors associated with seroreactivity against SFGR were male gender, older age, contact with backyard birds, and working in agriculture or with livestock. However, exposure to any kind of animal within the household decreased the odds ratio by half. Age was the only variable associated with higher TGR seroprevalence. The prevalence of Leptospira was 11.3% in Puerto Maldonado and 5.8% in Tumbes, with a borderline association with keeping animals in the household. We tested animal sera for Leptospira and conducted polymerase chain reaction (PCR) to detect Rickettsia species among ectoparasites collected from domestic animals in 63 households of seropositive participants and controls. We did not find any association between animal infection and human serostatus

Identification of Leptospira and Bartonella among rodents collected across a habitat disturbance gradient along the Inter-Oceanic Highway in the southern Amazon Basin of Peru.

BACKGROUND: The southern Amazon Basin in the Madre de Dios region of Peru has undergone rapid deforestation and habitat disruption, leading to an unknown zoonotic risk to the growing communities in the area. METHODOLOGY/PRINCIPAL FINDINGS: We surveyed the prevalence of rodent-borne Leptospira and Bartonella, as well as potential environmental sources of human exposure to Leptospira, in 4 communities along the Inter-Oceanic Highway in Madre de Dios. During the rainy and dry seasons of 2014-2015, we captured a total of 97 rodents representing 8 genera in areas that had experienced different degrees of habitat disturbance. Primarily by using 16S metagenomic sequencing, we found that most of the rodents (78%) tested positive for Bartonella, whereas 24% were positive for Leptospira; however, the patterns differed across seasons and the extent of habitat disruption. A high prevalence of Bartonella was identified in animals captured across both trapping seasons (72%-83%) and the relative abundance was correlated with increasing level of land disturbance. Leptospira-positive animals were more than twice as prevalent during the rainy season (37%) as during the dry season (14%). A seasonal fluctuation across the rainy, dry, and mid seasons was also apparent in environmental samples tested for Leptospira (range, 55%-89% of samples testing positive), and there was a high prevalence of this bacteria across all sites that were sampled in the communities. CONCLUSIONS/SIGNIFICANCE: These data indicate the need for increased awareness of rodent-borne disease and the potential for environmental spread along the communities in areas undergoing significant land-use change

Economic Burden of Dengue Virus Infection at the Household Level Among Residents of Puerto Maldonado, Peru.

Dengue virus (DENV) was reintroduced to Peru in the 1990s and has been reported in Puerto Maldonado (population ~65,000) in the Peruvian southern Amazon basin since 2000. This region also has the highest human migration rate in the country, mainly from areas not endemic for DENV. The objective of this study was to assess the proportion of household income that is diverted to costs incurred because of dengue illness and to compare these expenses between recent migrants (RMs) and long-term residents (LTRs). We administered a standardized questionnaire to persons diagnosed with dengue illness at Hospital Santa Rosa in Puerto Maldonado from December 2012 to March 2013. We compared direct and indirect medical costs between RMs and LTRs. A total of 80 participants completed the survey, of whom 28 (35%) were RMs and 52 (65%) were LTRs. Each dengue illness episode cost the household an average of US$105 (standard deviation [SD] = 107), representing 24$56, SD = 87), especially lost wages. The proportion of household income diverted to dengue illness did not differ significantly between RM and LTR households. The study highlights the significant financial burden incurred by households when a family member suffers dengue illness

Teenage Pregnancy in Tambogrande, Peru: Causes, Consequences and Cycles of Violence and Disadvantage

Teenage pregnancy carries adverse consequences for health and well-being. In this paper, we investigate the perceived causes, consequences and cycles of violence and disadvantage associated with teenage pregnancy in Tambogrande, Peru using an applied anthropological approach. Data were drawn from a larger project investigating the relationship between water insecurity and gender-based violence in Indonesia and Peru. The analysis presented here is derived from 49 semi-structured interviews and 5 focus groups with local community members and stakeholders in Peru. Study participants highlighted two main factors contributing to teenage pregnancy in Tambogrande: machismo and religious deterrents to contraceptive use. Participants described how these factors overlapped, resulting in gendered power imbalances that increased the risk of violence, decreased educational opportunities, and reduced the economic independence of women. However, study participants stated that educational interventions targeting machismo could reduce teenage pregnancy and break the associated cycle of disadvantage. Future research will further investigate local social and gender norms to inform the design of a rights-based educational intervention, targeting upstream factors associated with teenage pregnancy in this area