Resistance to colistin and carbapenem among Enterobacteriaceae recovered from human and animal sources is associated with multiple genetic mechanisms

Abstract

Colistin and carbapenem and are important last-resort antimicrobials to treat infections caused by multidrug-resistant Gram-negative bacteria. Understanding the genetic mechanisms conferring resistance to colistin and carbapenem and their prevalence are critical in the development of preventive measures. There is little information on resistance to colistin and carbapenem among Enterobacteriaceae in Nigeria and sub-Saharan Africa. Developing nations have poor sanitation practices and policies regulating use of antibiotics, enhancing the spread of antimicrobial resistance. The emergence of resistant bacteria to these last-resort drugs has necessitated a study to understand the genetic mechanisms conferring resistance and their prevalence, which is critical in the development of preventive and therapeutic measures. While there has been quite a number of investigations and good antimicrobial surveillance practices in the United States, very few reports are available about the colistin and carbapenem resistant bacteria in animals. The research in this thesis aims to investigate the prevalence of colistin and carbapenem resistance from human and animals in Nigeria, and from pigs in the USA, and understand the genetic mechanisms driving the resistance. A total of 1,119 human (stool from outpatients and urine from ICU patients) and animal (rectal swabs from cattle, dogs, pigs, poultry) samples were collected from Benue State, Northcentral, Nigeria. 583 non-duplicate Enterobacteriaceae were recovered from these samples using phenotypic methods and whole-genome sequencing (WGS). Of the 583 isolates, 17.0% (99/583) were resistant to colistin, 18.9% (110/583) were resistant to carbapenem, and 9.1% (53/583) had concurrent carbapenem-colistin resistance. PCR (mcr-1 to mcr-9) and whole-genome sequencing (WGS) identified mcr in 21.2% (21/99) of colistin-resistant isolates: mcr-1.1 (n = 13), mcr-8.1 (n = 5), mcr-1.1 and mcr-8.1 (n = 2), and mcr-1.1 and mcr-5 (n = 1). Of the 21 mcr-positive strains, 9 were isolated from human samples, with 8 being Klebsiella pneumoniae, and 6 of these human K. pneumoniae had a high colistin MIC (>64 μg/mL). In contrast, 9 of the 12 mcr-positive animal isolates were Escherichia coli, of which only 2 had a colistin MIC of >64 μg/mL. The carbapenem minimum inhibitory concentrations was between 2 and 32 µl/ml. Interestingly, none of the carbapenem resistant bacteria produced any carbapenemase genes. However, they had a combination of efflux pump mutations, outer membrane protein mutations, and production of extended spectrum beta-lactamases. The population structures of the bacterial isolates carrying concurrent colistin and carbapenem resistance were highly polyclonal, distributed into 37 different sequence types and characterized by the presence of internationally recognized high-risk clones in Klebsiella pneumoniae ST11, ST58, ST340-human isolates) and in E. coli (ST58, ST744, ST410 -animal isolates). Novel and existing mutations were also observed amongst the resistant isolates. Escherichia coli was the most commonly isolated organism from animal samples, while Klebsiella pneumoniae was most commonly isolated from human samples. On the contrary, of the 85 commercial swine fecal samples collected Auburn, Alabama, USA, carbapenem-resistant isolate was not identified. However, molecular analysis by FRET-PCR identified mcr genes from 34.5% (38/110) isolates, with mcr-2 gene as the most prominent 73.7% (28/38). Of the mcr positive isolates analyzed for speciation by 16S rRNA, E. coli (70.8%) was the most commonly isolated, followed by K. pneumoniae (25.0%), and Salmonella enterica (4.2%). In two of the mcr- positive isolates, WGS identified (marA, ampC, pmrC, pmrE, pmrF, and blaEC) known to confer multiple antibiotic resistance, and blaAMPH was identified in only one of the isolates. This study is the first to report mcr-1 in Alcaligenes faecalis and the emergence of mcr-5 and mcr-8 in Nigeria. WGS determined that mcr-1 was localized on an IncX4 plasmid and that 95.2% of mcr-1 harboring isolates (20/21) transferred colistin resistance successfully by conjugation. This study adds valuable information regarding resistance to colistin and carbapenem with implications for both human and animal health. These findings highlight the global spread of colistin resistance and emphasize the urgent need for coordinated global action to combat resistant bacteria. The presence of high-risk clones in these isolates provides worrisome evidence that humans and animals may serve as reservoirs and vectors for global microbial spread and should therefore be continuously monitored.