Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

Abstract

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.

Studies on Drug Resistance among Klebsiella and Citrobacter spp Isolated from two Human Groups and Wild Animals

“…High correlates of > 0.5 signifies that other factors such as the discharge of antibiotic contaminated wastewater effluents (25,26) among others may be responsible for the resistance exhibited against the antibiotics (Table 1). This is in line with previous researches that have adduced the presence of resistance to several factors including, but not limited to, environmental factors (19,27,28), selective pressure of antibiotics (29), genetic compatibility of microorganisms (30), etc. Reportedly, whether or not microorganisms were previously exposed to antibiotics, their intrinsic ability to pick up genetic material from their environment (16) is an indication that resistance could be conferred on an organism through various means (31).…”

Regulation of conjugative transfer of plasmids and integrative conjugative elements

“…Since the 1960s, plasmids carrying antibiotic resistance genes have continuously gained interest (Wyrsch et al, 2016), moreover, pollution in different regions of the planet has led to the discovery and description of plasmids involved in metal resistance (Aminov, 2011). Plasmids involved in pathogenic (Aviv et al, 2016;Lang and Faure, 2014) and symbiotic interactions are also widely known (Romero and Brom, 2004).…”

“…They may contain genes conferring resistance to antibiotics and metals, the utilization of carbon compounds, virulence or symbiosis determinants (Dejonghe et al, 2000;Heuer and Smalla, 2012;Top et al, 1995;Wyrsch et al, 2016).…”

Novel Antibiotic Resistance Determinants from Agricultural Soil Exposed to Antibiotics Widely Used in Human Medicine and Animal Farming

“…FolP SMZ B27 is distantly related (ϳ30% shared sequence identity) to three highly prevalent sulfonamide-resistant DHPS alternatives, Sul1, Sul2, and Sul3 (32), and shows the greatest homology with deduced DHPSs of several uncultured bacteria belonging to the candidate phyla radiation (CPR) group (Fig. 6).…”