Feasibility, enablers and challenges of using timeliness metrics for household contact tracing and TB preventive therapy in Pakistan.

INTRODUCTION: Screening household contacts of TB patients and providing TB preventive therapy (TPT) is a key intervention to end the TB epidemic. Global and timely implementation of TPT in household contacts, however, is dismal. We adapted the 7-1-7 timeliness metric designed to evaluate and respond to infectious disease outbreaks or pandemics, and assessed the feasibility, enablers and challenges of implementing this metric for screening and management of household contacts of index patients with bacteriologically-confirmed pulmonary TB in Karachi city, Pakistan. METHODS: We conducted an explanatory mixed methods study with a quantitative component (cohort design) followed by a qualitative component (descriptive design with focus group discussions). RESULTS: From January-June 2023, 92% of 450 index patients had their household contacts line-listed within seven days of initiating anti-TB treatment ("first 7"). In 84% of 1342 household contacts, screening outcomes were ascertained within one day of line-listing ("next 1"). In 35% of 256 household contacts eligible for further evaluation by a medical officer (aged ≤5 years or with chest symptoms), anti-tuberculosis treatment, TPT or a decision for no drugs was made within seven days of symptom screening ("second 7"). The principal reason for not starting anti-tuberculosis treatment or TPT was failure to consult a medical officer: only 129(50%) of 256 contacts consulted a medical officer. Reasons for poor performance in the "second 7" component included travel costs to see a medical officer, loss of daily earnings and fear of a TB diagnosis. Field staff reported that timeliness metrics motivated them to take prompt action in household contact screening and TPT provision and they suggested these be included in national guidelines. CONCLUSIONS: Field staff found "7-1-7" timeliness metrics to be feasible and useful. Integration of these metrics into national guidelines could improve timeliness of diagnosis, treatment and prevention of TB within households of index patients.

The Trend, Characteristics and Treatment Outcomes in Patients with Tuberculosis Undergoing Thoracic Surgery in the Kyrgyz Republic between 2017 and 2021.

Surgery has played an important role in managing complicated tuberculosis in former Soviet Union countries, including the Kyrgyz Republic. However, published information is limited. This study aimed to document the trend, characteristics and outcomes of tuberculosis patients who underwent thoracic surgery, using routinely collected data. Between 2017 and 2021, 4-7% of tuberculosis patients in the Kyrgyz Republic underwent thoracic surgery in two centres in Bishkek and Osh. In 2021, case records were retrieved in 264 (78%) of 340 patients undergoing thoracic surgery in the country. The most common indications for surgery were pleural exudate/empyema in 127 (44%) and tuberculoma in 83 (32%). Most patients (73%) underwent surgery within 30 days of starting TB treatment. Two-thirds of patients underwent radical surgery, and surgical outcomes were excellent in 99% of patients with one death. Post-operatively, 63 (23%) patients had no TB detected by the histology, with the two most common specified conditions being lung cancer and pulmonary hydatid disease. TB treatment was stopped in these patients. Of the 201 patients with confirmed TB after surgery, TB-treatment success was documented in 163 (81%), died/failure/lost to follow-up in 10 (5%) and not evaluated in 28 (14%). This study shows that thoracic surgery is feasible, safe and effective in the routine programme setting. Recommendations are made to strengthen referral and monitoring systems.

Global, regional, and national estimates of tuberculosis incidence and case detection among incarcerated individuals from 2000 to 2019: a systematic analysis.

BACKGROUND: People who are incarcerated are at high risk of developing tuberculosis. We aimed to estimate the annual global, regional, and national incidence of tuberculosis among incarcerated populations from 2000 to 2019. METHODS: We collected and aggregated data for tuberculosis incidence and prevalence estimates among incarcerated individuals in published and unpublished literature, annual tuberculosis notifications among incarcerated individuals at the country level, and the annual number of incarcerated individuals at the country level. We developed a joint hierarchical Bayesian meta-regression framework to simultaneously model tuberculosis incidence, notifications, and prevalence from 2000 to 2019. Using this model, we estimated trends in absolute tuberculosis incidence and notifications, the incidence and notification rates, and the case detection ratio by year, country, region, and globally. FINDINGS: In 2019, we estimated a total of 125 105 (95% credible interval [CrI] 93 736-165 318) incident tuberculosis cases among incarcerated individuals globally. The estimated incidence rate per 100 000 person-years overall was 1148 (95% CrI 860-1517) but varied greatly by WHO region, from 793 (95% CrI 430-1342) in the Eastern Mediterranean region to 2242 (1515-3216) in the African region. Global incidence per 100 000 person-years between 2000 and 2012 among incarcerated individuals decreased from 1884 (95% CrI 1394-2616) to 1205 (910-1615); however, from 2013 onwards, tuberculosis incidence per 100 000 person-years was stable, from 1183 (95% CrI 876-1596) in 2013 to 1148 (860-1517) in 2019. In 2019, the global case detection ratio was estimated to be 53% (95% CrI 42-64), the lowest over the study period. INTERPRETATION: Our estimates suggest a high tuberculosis incidence rate among incarcerated individuals globally with large gaps in tuberculosis case detection. Tuberculosis in incarcerated populations must be addressed with interventions specifically tailored to improve diagnoses and prevent transmission as a part of the broader global tuberculosis control effort. FUNDING: National Institutes of Health.

Contact Tracing and Tuberculosis Preventive Therapy for Household Child Contacts of Pulmonary Tuberculosis Patients in the Kyrgyz Republic: How Well Are We Doing?

Early identification, screening and investigation for tuberculosis (TB), and provision of TB preventive therapy (TPT), reduces risk of TB among child household contacts of pulmonary TB patients (index patients). A cohort study was conducted to describe the care cascade and timeliness of contact tracing and TPT initiation among child household contacts (aged < 15 years) of index patients initiated on TB treatment in Bishkek, the Kyrgyz Republic during October 2021-September 2022. In the register, information on the number of child household contacts was available for 153 (18%) of 873 index patients. Of 297 child household contacts identified, data were available for 285, of whom 261 (92%) were screened for TB. More than 50% were screened after 1 month of the index patient initiating TB treatment. TB was diagnosed in 23/285 (9%, 95% CI: 6-13%) children. Of 238 TB-free children, 130 (55%) were eligible for TPT. Of the latter, 64 (49%) were initiated on TPT, of whom 52 (81%) completed TPT. While TPT completion was excellent, there was deficiency in contact identification, timely screening and TPT initiation. Thus, healthcare providers should diligently request and record details of child household contacts, adhere to contact tracing timelines and counsel caregivers regarding TPT.

Strengthening the Operational Research Capacity of National Tuberculosis Control Programs: Necessity or Luxury?

'How to get research into practice: first get practice into research [...].

Managing Comorbidities, Determinants and Disability at Start and End of TB Treatment under Routine Program Conditions in China.

Many patients with tuberculosis (TB) have comorbidities, risk determinants and disability that co-exist at diagnosis, during and after TB treatment. We conducted an observational cohort study in 11 health facilities in China to assess under routine program conditions (i) the burden of these problems at the start and end of TB treatment and (ii) whether referral mechanisms for further care were functional. There were 603 patients registered with drug-susceptible TB who started TB treatment: 84% were symptomatic, 14% had diabetes, 14% had high blood pressure, 19% smoked cigarettes, 10% drank excess alcohol and in 45% the 6 min walking test (6MWT) was abnormal. Five patients were identified with mental health disorders. There were 586 (97%) patients who successfully completed TB treatment six months later. Of these, 18% were still symptomatic, 12% had diabetes (the remainder with diabetes failed to complete treatment), 5% had high blood pressure, 5% smoked cigarettes, 1% drank excess alcohol and 25% had an abnormal 6MWT. Referral mechanisms for the care of comorbidities and determinants worked well except for mental health and pulmonary rehabilitation for disability. There is need for more programmatic-related studies in other countries to build the evidence base for care of TB-related conditions and disability.

Colistin resistance in Escherichia coli and Klebsiella pneumoniae in humans and backyard animals in Ecuador.

Objective: Colistin is an antibiotic of last resort for treating serious Gram-negative bacterial infections. However, the misuse of colistin, especially as an animal growth promoter, has contributed to increasing antimicrobial resistance, mediated mainly through plasmid transfer of the mcr-1 gene. This study assessed the prevalence of phenotypic and molecular colistin resistance in Escherichia coli and Klebsiella pneumoniae in Ecuador in healthy humans and their chickens and pigs. Methods: Fecal samples were collected from humans and their chickens and pigs in two rural coastal and Amazon regions between April and August 2020. Gram-negative bacteria were isolated and identified using conventional techniques. Phenotypic resistance was determined using the broth microdilution technique, and the mcr-1 gene was detected using conventional polymerase chain reaction. Results: A total of 438 fecal samples were obtained from 137 humans, 147 pigs and 154 chickens. The prevalence of E. coli isolates was 86.3% (378/438) and K. pneumoniae, 37.4% (164/438). Overall, the mcr-1 gene was found in 90% (340/378) of E. coli isolates, with higher prevalences found in isolates from coastal regions (96.5%, 191/198), humans (95.6%, 111/116) and chickens (91.8%, 123/134); for K. pneumoniae, the gene was found in 19.5% (32/164) of isolates, with equal distribution between regions and hosts. Only four isolates, two E. coli and two K. pneumoniae, showed phenotypic resistance: mcr-1 was present in both E. coli strains but absent in the K. pneumoniae strains. Conclusions: Despite a low prevalence of phenotypic resistance to colistin, the high prevalence of the mcr-1 gene in E. coli is of concern. Ecuador's ban on using colistin in animal husbandry must be enforced, and continual monitoring of the situation should be implemented.

Whole-genome sequencing for surveillance of antimicrobial resistance in Ecuador: present and future implications.

Whole-genome sequencing is becoming the gold standard for pathogen characterization and offers considerable advantages for understanding the evolution and dissemination of new determinants of antimicrobial resistance. Despite the benefits of whole-genome sequencing for pathogen characterization, implementation costs and lack of expertise may limit its use by public health laboratories. This article reviews the advantages of whole-genome sequencing for pathogen characterization and the current status of the use of whole-genome sequencing for antimicrobial resistance surveillance in Ecuador. A roadmap is suggested for including whole-genome sequencing for pathogen characterization based on the needs of the health reference institutions through alliances with Ecuadorian universities. Establishing a partnership between public health institutions and academia would be valuable for clinicians, policy-makers, and epidemiologists who could then take reasonable measures in those areas and establish a basis for adapting One Health strategies to tackle antimicrobial resistance in Ecuador.

La secuenciación del genoma completo, que está pasando a ser el estándar de referencia para la caracterización de agentes patógenos, ofrece ventajas considerables para comprender la evolución y la diseminación de los nuevos determinantes de la resistencia a los antimicrobianos. Sin embargo, a pesar de los beneficios que genera, los costos de ejecución y la falta de experiencia pueden limitar su uso por parte de los laboratorios de salud pública. En este artículo se evalúan las ventajas de la secuenciación del genoma completo para la caracterización de agentes patógenos y el estado actual del uso de la secuenciación del genoma completo en la vigilancia de la resistencia a los antimicrobianos en Ecuador. Se propone una hoja de ruta para incluir la secuenciación del genoma completo para la caracterización de agentes patógenos según las necesidades de las instituciones de salud de referencia, lo que se haría por medio de alianzas con universidades ecuatorianas. Establecer una asociación entre las instituciones de salud pública y los círculos académicos sería sumamente valioso para los médicos, los responsables de las políticas y los epidemiólogos, que podrían adoptar medidas razonables en sus ámbitos y sentar una base para adaptar las estrategias de "Una salud" a fin de abordar la resistencia a los antimicrobianos en Ecuador.

O sequenciamento do genoma completo está se tornando o padrão ouro para a caracterização de patógenos e oferece vantagens consideráveis para a compreensão da evolução e disseminação de novos determinantes de resistência aos antimicrobianos. Apesar dos benefícios do sequenciamento do genoma completo para a caracterização de patógenos, os custos de implementação e a falta de especialização podem limitar seu uso pelos laboratórios de saúde pública. Este artigo analisa as vantagens do sequenciamento do genoma completo para a caracterização de patógenos e a situação atual do uso desta técnica para a vigilância da resistência aos antimicrobianos no Equador. Sugere-se um roteiro para incluir o sequenciamento de genomas completos para caracterização de patógenos com base nas necessidades das instituições de saúde de referência, por meio de alianças com universidades equatorianas. A criação de uma parceria entre instituições de saúde pública e entidades acadêmicas seria valiosa para clínicos, formuladores de políticas e epidemiologistas, que poderiam, assim, tomar medidas razoáveis nessas áreas e estabelecer uma base para adaptar estratégias de Saúde Única para combater a resistência aos antimicrobianos no Equador.

Colistin resistance in Escherichia coli and Klebsiella pneumoniae in humans and backyard animals in Ecuador

[ABSTRACT]. Objective. Colistin is an antibiotic of last resort for treating serious Gram-negative bacterial infections. However, the misuse of colistin, especially as an animal growth promoter, has contributed to increasing antimicrobial resistance, mediated mainly through plasmid transfer of the mcr-1 gene. This study assessed the prevalence of phenotypic and molecular colistin resistance in Escherichia coli and Klebsiella pneumoniae in Ecuador in healthy humans and their chickens and pigs. Methods. Fecal samples were collected from humans and their chickens and pigs in two rural coastal and Amazon regions between April and August 2020. Gram-negative bacteria were isolated and identified using conventional techniques. Phenotypic resistance was determined using the broth microdilution technique, and the mcr-1 gene was detected using conventional polymerase chain reaction. Results. A total of 438 fecal samples were obtained from 137 humans, 147 pigs and 154 chickens. The preva- lence of E. coli isolates was 86.3% (378/438) and K. pneumoniae, 37.4% (164/438). Overall, the mcr-1 gene was found in 90% (340/378) of E. coli isolates, with higher prevalences found in isolates from coastal regions (96.5%, 191/198), humans (95.6%, 111/116) and chickens (91.8%, 123/134); for K. pneumoniae, the gene was found in 19.5% (32/164) of isolates, with equal distribution between regions and hosts. Only four isolates, two E. coli and two K. pneumoniae, showed phenotypic resistance: mcr-1 was present in both E. coli strains but absent in the K. pneumoniae strains. Conclusions. Despite a low prevalence of phenotypic resistance to colistin, the high prevalence of the mcr-1 gene in E. coli is of concern. Ecuador’s ban on using colistin in animal husbandry must be enforced, and con- tinual monitoring of the situation should be implemented.

[RESUMEN]. Objetivo. La colistina es un antibiótico de último recurso para tratar infecciones graves por bacterias gramneg- ativas. Sin embargo, su uso indebido, especialmente para estimular el crecimiento animal, ha contribuido con el aumento de la resistencia a los antimicrobianos, mediada principalmente por la transferencia de plásmidos del gen mcr-1. En este estudio se evaluó la prevalencia de la resistencia fenotípica y molecular a la colistina de las bacterias Escherichia coli y Klebsiella pneumoniae en humanos sanos, sus pollos y cerdos en Ecuador. Métodos. Se recolectaron muestras fecales de humanos, así como de sus pollos y cerdos, en dos zonas rurales de la región costera y la región amazónica entre abril y agosto del 2020. Se aislaron las bacterias gramnegativas y se identificaron empleando técnicas convencionales. Se determinó la resistencia fenotípica mediante la técnica de microdilución en caldo y se detectó el gen mcr-1 con la técnica convencional de reac- ción en cadena de la polimerasa. Resultados. Se obtuvo un total de 438 muestras fecales de 137 humanos, 147 cerdos y 154 pollos. La preva- lencia de E. coli en las cepas aisladas fue del 86,3% (378/438) y la de K. pneumoniae, del 37,4% (164/438). En general, se detectó el gen mcr-1 en el 90% (340/378) de las cepas aisladas de E. coli y la mayor prevalencia encontrada fue en cepas aisladas de la región costera (96,5%, 191/198), humanos (95,6%, 111/116) y pollos (91,8%, 123/134); en el caso de K. pneumoniae, el gen se encontró en el 19,5% (32/164) de las cepas, con una distribución equitativa entre regiones y hospedadores. Únicamente cuatro cepas aisladas, dos de E. coli y dos de K. pneumoniae, mostraron resistencia fenotípica: el gen mcr-1 estaba presente en ambas cepas de E. coli y ausente en las cepas de K. pneumoniae. Conclusiones. Si bien hubo una baja prevalencia de resistencia fenotípica a la colistina, la alta prevalencia del gen mcr-1 en E. coli es preocupante. Es necesario hacer cumplir la prohibición del uso de colistina en la cría de animales en Ecuador, así como realizar un seguimiento continuo de la situación.

[RESUMO]. Objetivo. A colistina é um antibiótico de último recurso para o tratamento de infecções graves por bac- térias Gram-negativas. Entretanto, o uso indevido da colistina, principalmente como promotor de crescimento animal, tem contribuído para o aumento da resistência a antimicrobianos, principalmente por transferência horizontal do gene mcr-1 mediada por plasmídeos. Este estudo avaliou a prevalência de resistência fenotípica e molecular à colistina em Escherichia coli e Klebsiella pneumoniae no Equador em humanos hígidos e em galinhas e porcos por eles criados. Métodos. Entre abril e agosto de 2020, foram coletadas amostras de fezes de habitantes de duas regiões litorâneas e amazônicas do Equador e de galinhas e porcos por eles criados. Bactérias Gram-negativas foram isoladas e identificadas por meio de técnicas convencionais. A resistência fenotípica foi determinada pela técnica de microdiluição em caldo, e o gene mcr-1 foi detectado por reação em cadeia da polimerase convencional. Resultados. Foram obtidas 438 amostras fecais de 137 humanos, 147 suínos e 154 galinhas. A prevalência de isolados de E. coli foi de 86,3% (378/438), e de K. pneumoniae, 37,4% (164/438). Em geral, o gene mcr-1 foi encontrado em 90% (340/378) dos isolados de E. coli, com maiores prevalências encontradas em isola- dos de regiões litorâneas (96,5%, 191/198), humanos (95,6%, 111/116) e galinhas (91,8%, 123/134); para K. pneumoniae, o gene foi encontrado em 19,5% (32/164) dos isolados, com igual distribuição entre regiões e hospedeiros. Somente quatro isolados, dois de E. coli e dois de K. pneumoniae, demonstraram resistência fenotípica: o gene mcr-1 estava presente em ambas as cepas de E. coli, mas ausente nas de K. pneumoniae. Conclusões. Apesar da baixa prevalência de resistência fenotípica à colistina, a alta prevalência do gene mcr-1 em E. coli é preocupante. É preciso fiscalizar a proibição ao uso agropecuário de colistina no Equador e implementar o monitoramento contínuo da situação.

Empanelment of the Population to the Primary Medical Care Institution of Sri Lanka: A Mixed-Methods Study on Outcomes and Challenges.

The registration of individuals with designated primary medical care institutions (PMCIs) is a key step towards their empanelment with these PMCIs, supported by the Primary Health Care System Strengthening Project in Sri Lanka. We conducted an explanatory mixed-methods study to assess the extent of registration at nine selected PMCIs and understand the challenges therein. By June 2021, 36,999 (19.2%, 95% CI-19.0-19.4%) of the 192,358 catchment population allotted to these PMCIs were registered. At this rate, only 50% coverage would be achieved by the end of the project (December 2023). Proportions of those aged <35 years and males among those registered were lower compared to their general population distribution. Awareness activities regarding registration were conducted in most of the PMCIs, but awareness in the community was low. Poor registration coverage was due to a lack of dedicated staff for registration, misconceptions of health care workers about individuals needing to be registered, reliance on opportunistic or passive registration, and lack of monitoring mechanisms; these were further compounded by the COVID-19 pandemic. Moving forward, there is an urgent need to address these challenges to improve registration coverage and ensure that all individuals are empaneled before the close of the project for it to have a meaningful impact.

Increased All-cause Mortality in People With HIV and Comorbidities: Hepatitis B and C Virus Seropositivity and Hyperglycemia in Myanmar, 2005-2017.

Background: Hepatitis C virus (HCV) and hepatitis B virus (HBV) coinfection are associated with increased mortality in people with HIV (PWH), and hyperglycemia is a common comorbidity in PWH. In this study, we used routinely collected clinical data to assess the associations between HBV and HCV seropositivity with all-cause mortality and whether this relationship differs by hyperglycemia status. Methods: Eligible participants included adult PWH (≥15 years) who initiated antiretroviral therapy between May 2005 and June 2016 in Myanmar. HBV and HCV serostatus and hyperglycemia were measured at enrollment to HIV care using HBV surface antigen, HCV antibody tests, and random blood glucose (≥140 mg/dL), respectively. Results: Among 27 722 PWH, 2260 (8%) were HBV seropositive, 2265 (9%) were HCV seropositive, 178 (0.6%) were HBV-HCV seropositive, and 1425 (5%) had hyperglycemia. During the median follow-up (interquartile range) of 3.1 (1.5-5.1) years, 3655 (13%) PWH died, and the overall mortality rate was 3.8 (95% CI, 3.7-3.9) per 100-person-years (PY). The mortality rate (per 100 PY) among PWH who were HBV seropositive was 4.6, among PWH who were HCV seropositive it was 5.1, and among PWH who were HBV-HCV seropositive it was 7.1. When stratified by glycemic status, the mortality rate was higher among patients with hyperglycemia compared with those with euglycemia (5.4 vs 4.0 per 100 PY), and the difference in mortality rate between patients with hyperglycemia and euglycemia was highest among those with HCV seropositivity (9.8 vs 5.0 per 100 PY). Conclusions: Increased mortality rates associated with HBV and HCV seropositivity in PWH differed by their glycemic status. PWH with HCV seropositivity and hyperglycemia had the highest mortality rates.

Outcomes and Challenges in Noncommunicable Disease Care Provision in Health Facilities Supported by Primary Health Care System Strengthening Project in Sri Lanka: A Mixed-Methods Study.

The Primary Healthcare System Strengthening Project in Sri Lanka focuses on improving noncommunicable disease (NCD) care provision at primary medical care institutions (PMCIs). We conducted an explanatory mixed-methods study to assess completeness of screening for NCD risk, linkage to care, and outcomes of diabetes/hypertension care at nine selected PMCIs, as well as to understand reasons for gaps. Against a screening coverage target of 50% among individuals aged ≥ 35 years, PMCIs achieved 23.3% (95% CI: 23.0-23.6%) because of a lack of perceived need for screening among the public and COVID-19-related service disruptions. Results of investigations and details of further referral were not documented in almost half of those screened. Post screening, 45% of those eligible for follow-up NCD care were registered at medical clinics. Lack of robust recording/tracking mechanisms and preference for private providers contributed to post-screening attrition. Follow-up biochemical investigations for monitoring complications were not conducted in more than 50% of diabetes/hypertension patients due to nonprescription of investigations by healthcare providers and poor uptake among patients because of nonavailability of investigations at PMCI, requiring them to avail services from the private sector, incurring out-of-pocket expenditure. Primary care strengthening needs to address these challenges to ensure successful integration of NCD care within PMCIs.

Short Research Article: Do demographic, socioeconomic and clinical characteristics influence the number of psychological intervention sessions attended by young people in need of mental health care?

BACKGROUND AND METHOD: A cohort study using secondary data assessed associations between baseline characteristics and psychological sessions attended in young persons discharged from a Children and Young People's Mental Health Service in 2019. RESULTS: There were 584 persons who attended a median of seven sessions. On multivariable regression analysis, males attended fewer sessions than females, young people from more affluent communities attended more sessions than those from poorer communities and those presenting with eating disorders and self-harm in particular attended more sessions than those with anxiety. CONCLUSIONS: Addressing why these associations occur may improve mental health care in young persons.

Colistin resistance in Escherichia coli and Klebsiella pneumoniae in humans and backyard animals in Ecuador / Resistencia a la colistina de las bacterias Escherichia coli y Klebsiella pneumoniae en humanos y animales de granja en Ecuador / Resistência à colistina em Escherichia coli e Klebsiella pneumoniae em humanos e animais de quintal no Equador

ABSTRACT Objective. Colistin is an antibiotic of last resort for treating serious Gram-negative bacterial infections. However, the misuse of colistin, especially as an animal growth promoter, has contributed to increasing antimicrobial resistance, mediated mainly through plasmid transfer of the mcr-1 gene. This study assessed the prevalence of phenotypic and molecular colistin resistance in Escherichia coli and Klebsiella pneumoniae in Ecuador in healthy humans and their chickens and pigs. Methods. Fecal samples were collected from humans and their chickens and pigs in two rural coastal and Amazon regions between April and August 2020. Gram-negative bacteria were isolated and identified using conventional techniques. Phenotypic resistance was determined using the broth microdilution technique, and the mcr-1 gene was detected using conventional polymerase chain reaction. Results. A total of 438 fecal samples were obtained from 137 humans, 147 pigs and 154 chickens. The prevalence of E. coli isolates was 86.3% (378/438) and K. pneumoniae, 37.4% (164/438). Overall, the mcr-1 gene was found in 90% (340/378) of E. coli isolates, with higher prevalences found in isolates from coastal regions (96.5%, 191/198), humans (95.6%, 111/116) and chickens (91.8%, 123/134); for K. pneumoniae, the gene was found in 19.5% (32/164) of isolates, with equal distribution between regions and hosts. Only four isolates, two E. coli and two K. pneumoniae, showed phenotypic resistance: mcr-1 was present in both E. coli strains but absent in the K. pneumoniae strains. Conclusions. Despite a low prevalence of phenotypic resistance to colistin, the high prevalence of the mcr-1 gene in E. coli is of concern. Ecuador's ban on using colistin in animal husbandry must be enforced, and continual monitoring of the situation should be implemented.

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RESUMO Objetivo. A colistina é um antibiótico de último recurso para o tratamento de infecções graves por bactérias Gram-negativas. Entretanto, o uso indevido da colistina, principalmente como promotor de crescimento animal, tem contribuído para o aumento da resistência a antimicrobianos, principalmente por transferência horizontal do gene mcr-1 mediada por plasmídeos. Este estudo avaliou a prevalência de resistência fenotípica e molecular à colistina em Escherichia coli e Klebsiella pneumoniae no Equador em humanos hígidos e em galinhas e porcos por eles criados. Métodos. Entre abril e agosto de 2020, foram coletadas amostras de fezes de habitantes de duas regiões litorâneas e amazônicas do Equador e de galinhas e porcos por eles criados. Bactérias Gram-negativas foram isoladas e identificadas por meio de técnicas convencionais. A resistência fenotípica foi determinada pela técnica de microdiluição em caldo, e o gene mcr-1 foi detectado por reação em cadeia da polimerase convencional. Resultados. Foram obtidas 438 amostras fecais de 137 humanos, 147 suínos e 154 galinhas. A prevalência de isolados de E. coli foi de 86,3% (378/438), e de K. pneumoniae, 37,4% (164/438). Em geral, o gene mcr-1 foi encontrado em 90% (340/378) dos isolados de E. coli, com maiores prevalências encontradas em isolados de regiões litorâneas (96,5%, 191/198), humanos (95,6%, 111/116) e galinhas (91,8%, 123/134); para K. pneumoniae, o gene foi encontrado em 19,5% (32/164) dos isolados, com igual distribuição entre regiões e hospedeiros. Somente quatro isolados, dois de E. coli e dois de K. pneumoniae, demonstraram resistência fenotípica: o gene mcr-1 estava presente em ambas as cepas de E. coli, mas ausente nas de K. pneumoniae. Conclusões. Apesar da baixa prevalência de resistência fenotípica à colistina, a alta prevalência do gene mcr-1 em E. coli é preocupante. É preciso fiscalizar a proibição ao uso agropecuário de colistina no Equador e implementar o monitoramento contínuo da situação.

Whole-genome sequencing for surveillance of antimicrobial resistance in Ecuador: present and future implications / Secuenciación del genoma completo para la vigilancia de la resistencia a los antimicrobianos en Ecuador: implicaciones actuales y futuras / Sequenciamento do genoma completo para vigilância da resistência aos antimicrobianos no Equador: implicações presentes e futuras

ABSTRACT Whole-genome sequencing is becoming the gold standard for pathogen characterization and offers considerable advantages for understanding the evolution and dissemination of new determinants of antimicrobial resistance. Despite the benefits of whole-genome sequencing for pathogen characterization, implementation costs and lack of expertise may limit its use by public health laboratories. This article reviews the advantages of whole-genome sequencing for pathogen characterization and the current status of the use of whole-genome sequencing for antimicrobial resistance surveillance in Ecuador. A roadmap is suggested for including whole-genome sequencing for pathogen characterization based on the needs of the health reference institutions through alliances with Ecuadorian universities. Establishing a partnership between public health institutions and academia would be valuable for clinicians, policy-makers, and epidemiologists who could then take reasonable measures in those areas and establish a basis for adapting One Health strategies to tackle antimicrobial resistance in Ecuador.

RESUMEN La secuenciación del genoma completo, que está pasando a ser el estándar de referencia para la caracterización de agentes patógenos, ofrece ventajas considerables para comprender la evolución y la diseminación de los nuevos determinantes de la resistencia a los antimicrobianos. Sin embargo, a pesar de los beneficios que genera, los costos de ejecución y la falta de experiencia pueden limitar su uso por parte de los laboratorios de salud pública. En este artículo se evalúan las ventajas de la secuenciación del genoma completo para la caracterización de agentes patógenos y el estado actual del uso de la secuenciación del genoma completo en la vigilancia de la resistencia a los antimicrobianos en Ecuador. Se propone una hoja de ruta para incluir la secuenciación del genoma completo para la caracterización de agentes patógenos según las necesidades de las instituciones de salud de referencia, lo que se haría por medio de alianzas con universidades ecuatorianas. Establecer una asociación entre las instituciones de salud pública y los círculos académicos sería sumamente valioso para los médicos, los responsables de las políticas y los epidemiólogos, que podrían adoptar medidas razonables en sus ámbitos y sentar una base para adaptar las estrategias de "Una salud" a fin de abordar la resistencia a los antimicrobianos en Ecuador.

RESUMO O sequenciamento do genoma completo está se tornando o padrão ouro para a caracterização de patógenos e oferece vantagens consideráveis para a compreensão da evolução e disseminação de novos determinantes de resistência aos antimicrobianos. Apesar dos benefícios do sequenciamento do genoma completo para a caracterização de patógenos, os custos de implementação e a falta de especialização podem limitar seu uso pelos laboratórios de saúde pública. Este artigo analisa as vantagens do sequenciamento do genoma completo para a caracterização de patógenos e a situação atual do uso desta técnica para a vigilância da resistência aos antimicrobianos no Equador. Sugere-se um roteiro para incluir o sequenciamento de genomas completos para caracterização de patógenos com base nas necessidades das instituições de saúde de referência, por meio de alianças com universidades equatorianas. A criação de uma parceria entre instituições de saúde pública e entidades acadêmicas seria valiosa para clínicos, formuladores de políticas e epidemiologistas, que poderiam, assim, tomar medidas razoáveis nessas áreas e estabelecer uma base para adaptar estratégias de Saúde Única para combater a resistência aos antimicrobianos no Equador.

Primary Health Care System Strengthening Project in Sri Lanka: Status and Challenges with Human Resources, Information Systems, Drugs and Laboratory Services.

A Primary Healthcare-System-Strengthening Project (PSSP) is implemented by the Ministry of Health, Sri Lanka, with funding support from the World Bank for providing quality care through primary medical care institutions (PMCIs). We used an explanatory mixed-methods study to assess progress and challenges in human resources, drug availability, laboratory services and the health management information system (HMIS) at PMCIs. We conducted a checklist-based assessment followed by in-depth interviews of healthcare workers in one PMCI each in all nine provinces. All PMCIs had medical/nursing officers, but data entry operators (44%) and laboratory technicians (33%) were mostly not available. Existing staff were assigned additional responsibilities in PSSP, decreasing their motivation and efficiency. While 11/18 (61%) essential drugs were available in all PMCIs, buffer stocks were not maintained in >50% due to poor supply chain management and storage infrastructure. Only 6/14 (43%) essential laboratory investigations were available in >50% of PMCIs, non-availability was due to shortages of reagents/consumables and lack of sample collection−transportation system. The HMIS was installed in PMCIs but its usage was sub-optimal due to perceived lack of utility, few trained operators and poor internet connectivity. The PSSP needs to address these bottlenecks as a priority to ensure sustainability and successful scale-up.

What Is in the Salad? Escherichia coli and Antibiotic Resistance in Lettuce Irrigated with Various Water Sources in Ghana.

INTRODUCTION: Safety of the environment in which vegetables are grown, marketed and consumed is paramount as most are eaten raw. Irrigation sources include open drains and streams, which are often contaminated with human and animal waste due to poor sanitation infrastructure. In irrigated vegetable farms using such sources in Ghana, we assessed Escherichia coli counts, antibiotic resistance patterns and resistant genes on irrigated lettuce. METHODS: A cross-sectional study was conducted between January-May 2022, involving five major vegetable farms in Ghana. RESULTS: Escherichia coli was found in all 25 composite lettuce samples analyzed. Counts expressed in CFU/g ranged from 186 to 3000, with the highest counts found in lettuce irrigated from open drains (1670) and tap water using hose pipes (3000). Among all bacterial isolates, resistance ranged between 49% and 70% for the Watch group of antibiotics, 59% for the Reserved group and 82% were multidrug-resistant. Of 125 isolates, 60 (48%) were extended-spectrum beta-lactamase-producing, of which five (8%) had the blaTEM-resistant gene. CONCLUSIONS: Lettuce was contaminated with Escherichia coli with high levels of antibiotic resistance. We call on the Ghana Ministry of Food and Agriculture, Food and Drugs Authority and other stakeholders to support farmers to implement measures for improving vegetable safety.

Quality, Equity and Partnerships in Mixed Methods and Qualitative Research during Seven Years of Implementing the Structured Operational Research and Training Initiative in 18 Countries.

Introduction: Qualitative studies are often inadequately reported, making it difficult to judge their appropriateness for decision making in public health. We assessed the publication characteristics and quality of reporting of qualitative and mixed-method studies from the Structured Operational Research and Training Initiative (SORT IT), a global partnership for operational research capacity building. Methods: A cross-sectional analysis of publications to assess the qualitative component using an adapted version of the Consolidated Criteria for Reporting Qualitative Research (COREQ) checklist. Results: In 67 publications involving 18 countries, 32 journals and 13 public health themes, 55 were mixed-methods studies and 12 were qualitative studies. First authorship from low-and-middle-income (LMIC) countries was present in 64 (96%), LMIC last authorship in 55 (82%), and female first authorship in 30 (45%). The mean LMIC institutions represented per publication was five (range 1-11). Sixty-three (94%) publications were open access. Reporting quality was graded as 'good' to 'excellent' in 60 (89%) publications, 'fair' in five (8%) and 'poor' in two (3%). Conclusion: Most SORT IT publications adhered to COREQ standards, while supporting gender equity in authorship and the promotion of LMIC research leadership. SORT IT plays an important role in ensuring quality of evidence for decision making to improve public health.

Antimicrobial, Multi-Drug and Colistin Resistance in Enterobacteriaceae in Healthy Pigs in the Greater Accra Region of Ghana, 2022: A Cross-Sectional Study.

There is little published information on antimicrobial resistance (AMR) in animals in Ghana. We determined the prevalence and factors associated with AMR, multi-drug resistance (MDR-resistance to ≥3 antimicrobial classes) and colistin resistance in Enterobacteriaceae in healthy pigs in Accra, Ghana. Rectal swabs obtained from the pigs on 20 farms from January to March 2022, were examined for Escherichia coli, Enterobacter spp. and Klebsiella pneumoniae. AMR was determined using standard microbiological techniques and the mcr-1 gene detected through molecular analysis. Enterobacteriaceae were isolated from 197 of 200 pigs: these comprised 195 E. coli isolates, 38 Enterobacter spp. and 3 K. pneumoniae, either singly or combined. Over 60% of E. coli were resistant to tetracycline, with 27% and 34% being resistant to amoxicillin/clavulanic acid and ampicillin, respectively; 23% of E. coli and 5% of Enterobacter spp. exhibited MDR phenotypes. Phenotypic colistin resistance was found in 8% of E. coli and Enterobacter spp., with the mcr-1 gene detected in half. Our study findings should be incorporated into on-going AMR, MDR and colistin resistance surveillance programs in Ghana. We further advocate for tailored-specific education for pig farmers on animal antimicrobial use and for strengthened regulatory policy on antimicrobial usage and monitoring in the animal production industry.