No abstract

We report the emergence of a novel lineage of SARS-CoV-2 in South America, termed C.37. It presents a deletion in the ORF1a gene (Δ3675-3677), also found in variants of concern (VOCs) Alpha, Beta, and Gamma, and seven non-synonymous mutations in the Spike gene (Δ247-253, G75V, T76I, L452Q, F490S, T859N). Initially reported in Lima, Peru, in late December 2020, it now accounts for almost 100% of Peruvian genomes in April 2021. It is expanding in Chile and Argentina, and there is evidence of onward transmission in Colombia, Mexico, the USA, Germany, and Israel. On June 15, 2021, the World Health Organization designated C.37 as Variant of Interest (VOI) Lambda.

The widespread and poorly regulated use of antibiotics in animal production in low- and middle-income countries (LMICs) is increasingly associated with the emergence and dissemination of antibiotic resistance genes (ARGs) in retail animal products. Here, we compared Escherichia coli from chickens and humans with varying levels of exposure to chicken meat in a low-income community in the southern outskirts of Lima, Peru. We hypothesize that current practices in local poultry production result in highly resistant commensal bacteria in chickens that can potentially colonize the human gut. E. coli was isolated from cloacal swabs of non-organic (n = 41) and organic chickens (n = 20), as well as from stools of market chicken vendors (n = 23), non-vendors (n = 48), and babies (n = 60). 315 E. coli isolates from humans (n = 150) and chickens (n = 165) were identified, with chickens showing higher rates of multidrug-resistant and extended-spectrum beta-lactamase phenotypes. Non-organic chicken isolates were more resistant to most antibiotics tested than human isolates, while organic chicken isolates were susceptible to most antibiotics. Whole-genome sequencing of 118 isolates identified shared phylogroups between human and animal populations and 604 ARG hits across genomes. Resistance to florfenicol (an antibiotic commonly used as a growth promoter in poultry but not approved for human use) was higher in chicken vendors compared to other human groups. Isolates from non-organic chickens contained genes conferring resistance to clinically relevant antibiotics, including mcr-1 for colistin resistance, blaCTX-M ESBLs, and blaKPC-3 carbapenemase. Our findings suggest that E. coli strains from market chickens are a potential source of ARGs that can be transmitted to human commensals.

The role of domestic cats in the dynamics of SARS-CoV-2 remains poorly characterized, especially in epidemiologic contexts of countries with high viral transmission. Here, we report the first evidence of SARS-CoV-2 Lambda variant of interest in symptomatic domestic cats whose owners were diagnosed with COVID-19 in Lima, Peru, providing evidence that transmission of this new variant in domestic cats is occurring. More epidemiological studies are required to further characterize the role of domestic animals in the transmission dynamics of SARS-CoV-2.

Poultry farming represents Peru’s primary food animal production industry, where antimicrobial growth promoters are still commonly used, exerting selective pressure on intestinal microbial populations. Consumption and direct animal-to-human transmission have been reported, and farmworkers are at high risk of colonization with resistant bacteria. We conducted a cross-sectional survey among 54 farmworkers to understand their current antimicrobial resistance (AMR) awareness in Ica, Peru. To gain insight into the potential work-related risk of exposure to bacteria, we also measured the AMR rates in Escherichia coli isolated among 50 broiler chickens. Farmworkers were unaware of antimicrobial resistance (31.5%) or antibiotic resistance (16.7%) terms. Almost two-thirds (61%) consumed antibiotics during the previous month, and only 42.6% received a prescription from a healthcare professional. A total of 107 E. coli chicken isolates were obtained, showing a high frequency of multidrug-resistant (89.7%) and extended-spectrum beta-lactamase (ESBL) production (71.9%). Among ESBL-producer isolates, 84.4% carried the blaCTX-M gene. Results identified gaps in knowledge that reflect the need for interventions to increase antimicrobial awareness among poultry farmworkers. The high AMR rates among E. coli isolates highlight the need to reduce antimicrobial use in poultry farms. Our findings reveal a critical need for effective policy development and antimicrobial stewardship interventions in poultry production in Ica, Peru.

Providencia stuartii is an opportunistic pathogen of the Enterobacteriales order. Here, we report the 4,594,658-bp draft genome sequence of a New Delhi metallo-β-lactamase (NDM-1)-producing Providencia stuartii strain that was isolated from an emergency patient in a private clinic in Lima, Peru.

Here, we report a draft genome sequence of a bla KPC-2 -carrying Citrobacter braakii isolated from pediatric hospital effluent. Genome CF248 represents a multidrug-resistant C. braakii isolate derived from a clinical environment in Peru.

Mycobacterium gordonae is a nontuberculous mycobacterium found in diverse environments and is considered an opportunistic pathogen in immunocompromised patients. We report the draft genome sequence of a Mycobacterium gordonae strain isolated from a free-living amoeba found in a nosocomial environment in Lima, Peru.