Scientific evidence for the control of antimicrobial resistance

[Extract]. Antimicrobial resistance (AMR) is one of the greatest global threats to human health. It is estimated that by 2050, AMR will lead to approximately 10 million annual deaths worldwide. Considering the impact of AMR on reproductive capacity and food production, in addition to its direct effect on infected people, the world's population could drop by between 11 and 444 million inhabitants by 2050 if AMR control is not achieved. As migrations and shared economies lead to the transmission of resistant bacteria across borders, the impacts of AMR become regionally significant. In the United States, methicillin-resistant Staphylococcus aureus caused 10 600 deaths in 2017. In Latin American and Caribbean countries, information is available from studies conducted in hospitals and other health facilities on the prevalence of antimicrobial-resistant pathogens. In many hospitals in Mexico, Peru, and Colombia, for example, resistance to third-generation cephalosporins and fluoroquinolones in Escherichia coli isolates is reaching almost 60%. Moreover, the dynamics of colonization and infection of multidrug-resistant organisms (such as carbapenemaseproducing Klebsiella pneumoniae) are unique in endemic areas of Latin America, favoring spread and dissemination. [...

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities

Surveillance of Antimicrobial Resistance in Hospital Wastewater: Identification of Carbapenemase-Producing Klebsiella spp.

The objective of this study was to investigate the presence and persistence of carbapenemase-producing Klebsiella spp. isolated from wastewater and treated wastewater from two tertiary hospitals in Mexico. We conducted a descriptive cross-sectional study in two hospital wastewater treatment plants, which were sampled in February 2020. We obtained 30 Klebsiella spp. isolates. Bacterial identification was carried out by the Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometry (MALDI-TOF MS®) and antimicrobial susceptibility profiles were performed using the VITEK2® automated system. The presence of carbapenem resistance genes (CRGs) in Klebsiella spp. isolates was confirmed by PCR. Molecular typing was determined by pulsed-field gel electrophoresis (PFGE). High rates of Klebsiella spp. resistance to cephalosporins and carbapenems (80%) were observed in isolates from treated wastewater from both hospitals. The molecular screening by PCR showed the presence of blaKPC and blaOXA-48-like genes. The PFGE pattern separated the Klebsiella isolates into 19 patterns (A–R) with three subtypes (C1, D1, and I1). Microbiological surveillance and identification of resistance genes of clinically important pathogens in hospital wastewater can be a general screening method for early determination of under-detected antimicrobial resistance profiles in hospitals and early warning of outbreaks and difficult-to-treat infections

Risk factors for extended-spectrum b-lactamases-producing Escherichia coli urinary tract infections in a tertiary hospital

Objective. To assess the risks factors for urinary tract infections (UTIs) caused by Extended-Spectrum Beta-Lactamases (ESBLs)-producing E. coli and the molecular characterization of ESBLs. Materials and methods. A case-control study was performed to identify risk factors in consecutively recruited patients with UTIs caused by ESBLs or non-ESBLs-producing E. coli in a tertiary hospital in Mexico. Results. ESBLs-producing E. coli were isolated from 22/70 (31%) patients with E. coli UTIs over a three month period. All isolates were resistant to cephalosporins and quinolones but susceptible to carbapenems, amikacin and nitrofurantoin. Prior antibiotic treatment with more than two antibiotic families (OR=6.86; 95%CI 1.06-157.70; p=0.028), recurrent symptomatic UTIs (OR=5.60; 95%CI 1.88-17.87; p=0.001) and previous hospitalization (OR=5.06; 95%CI 1.64-17.69;p=0.002) were significant risk factors. Sixteen isolates harbored the beta-lactamase (bla)CTX-M-15 gene and five the blaTEM-1 gene. Conclusions. One of every three patients presented UTIs with ESBLs-producing beta-lactams and fluoroquinolone resistant E. coli. Risk factors and resistance patterns must be taken into account for developing antibiotic use policies in these setting

Antimicrobial Resistance Patterns and Clonal Distribution of <i>E</i>. <i>coli</i>, <i>Enterobacter</i> spp. and <i>Acinetobacter</i> spp. Strains Isolated from Two Hospital Wastewater Plants

The objective of this study was to determine the presence and persistence of antimicrobial-resistant enterobacteria and their clonal distribution in hospital wastewater. A descriptive cross-sectional study was carried out in wastewater from two Mexico City tertiary level hospitals. In February and March of 2020, eight wastewater samples were collected and 26 isolates of enterobacteria were recovered, 19 (73.1%) isolates were identified as E. coli, 5 (19.2%) as Acinetobacter spp. and 2 (7.7%) as Enterobacter spp. Antimicrobial susceptibility profiles were performed using the VITEK 2® automated system and bacterial identification was performed by the Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometry (MALDI-TOF MS®). ESBL genes were detected by polymerase chain reaction (PCR) and clonal distributions of isolates were determined by pulsed-field gel electrophoresis (PFGE). E. coli susceptibility to different classes of antimicrobials was analyzed and resistance was mainly detected as ESBLs and fluoroquinolones. One E. coli strain was resistant to doripenem, ertapenem, imipenem and meropenem. The analysis by PCR showed the presence of specific β-lactamases resistance genes (blaKPC, blaCTX-M). The PFGE separated the E. coli isolates into 19 different patterns (A–R). PFGE results of Acinetobacter spp. showed the presence of a majority clone A. Surveillance of antimicrobial resistance through hospital wastewater is an important tool for early detection of clonal clusters of clinically important bacteria with potential for dissemination

SARS-CoV-2 Wastewater Surveillance in Ten Cities from Mexico

We aimed to estimate the lead time and infection prevalence from SARS-CoV-2 wastewater (WW) monitoring compared with clinical surveillance data in Mexico to generate evidence about the feasibility of a large-scale WW surveillance system. We selected 10 WW treatment plants (WWTP) and 5 COVID-19 hospitals in major urban conglomerates in Mexico and collected biweekly 24-h flow-adjusted composite samples during October–November 2020. We concentrated WW samples by polyethylene glycol precipitation and employed quantitative PCR (RT-qPCR) assays, targeting the nucleoprotein (N1 and N2) genes. We detected and quantified SARS-CoV-2 RNA in 88% and 58% of the raw WW samples from WWTPs and COVID-19 hospitals, respectively. The WW RNA daily loads lead the active cases by more than one month in large and medium WWTP sites. WW estimated that cases were 2 to 20-fold higher than registered active cases. Developing a continuous monitoring surveillance system for SARS-CoV-2 community transmission through WW is feasible, informative, and recognizes three main challenges: (1) WW system data (catchment area, population served), (2) capacity to maintain the cold-chain and process samples, and (3) supplies and personnel to ensure standardized procedures