Multidrug-resistant gram-negative (MRGN) bacteria are a serious threat to global health. We used genomics to study MRGN obtained from houseflies in a tertiary Rwandan hospital. Our analysis revealed a high abundance of different MRGN including E. coli pathogenic lineage ST131 suggesting the important role of flies in disseminating highly virulent pathogens in clinical settings and beyond.
Multidrug-resistant gram-negative (MRGN) bacteria include Escherichia (E.) coli, Klebsiella spp., Enterobacter (E.) cloacae, Acinetobacter spp., and Pseudomonas (P.) aeruginosa, and others, and cause a variety of severe infections like diarrhea, pneumonia, sepsis, endocarditis and urinary tract infection (UTI). Studies estimate 700.000 fatalities caused by antibiotic-resistant pathogens each year with increasing numbers . In addition to their common occurrence as nosocomial pathogens, MRGN have been frequently found in livestock and the environment. Flies have only recently come into spotlight as carriers of resistant bacteria, and their major route of colonization stems from walking on contaminated surfaces . The detection of antibiotic-resistant E. coli from flies captured in a livestock facility was thus unsurprising . Another study has shown that houseflies from hospitals in the UK carried different bacteria resistant to antibiotics . We investigated if houseflies captured in a tertiary hospital in Rwanda carried clinically relevant MRGN pathogens. In African hospital settings, where hygienic conditions may be suboptimal , flies might function as underestimated vectors for the distribution of antibiotic-resistant bacteria.
Overall 48% (20/42) of flies carried antibiotic-resistant bacteria. Thirty-six percent (15/42) carried ESBL-producing E. coli, 19% (8/42) E. cloacae, 9% (4/42) K. oxytoca, 7% (3/42) C. freundii, 4% (2/42) R. ornithinolytica, 4% (2/42) P. aeruginosa, and 2% (1/42) A. baumannii. Twelve flies (29%) carried more than one antibiotic-resistant bacterial genus of which three (F6, F9 and F18) carried three different pathogens (Fig. 1a/b).
All strains were phenotypically multidrug-resistant and thus termed MRGN (Fig. 1a), however they were not resistant to carbapenems or colistin. WGS revealed carriage of different antimicrobial resistance genes such as blaCTX-M-15,aac -IIa, and tet(A)/(B) (Table S1). Eight different STs were observed including ST131 and ST410 (Fig. 1b). Interestingly, these represent international high-risk clonal lineages [7, 8], which combine antimicrobial resistance with high-level virulence. The ST131 strain harbored ten resistance genes and 31 virulence-associated genes including the pap operon linked to UTI  (Table S1).
In addition, we observed five E. coli strains of ST5474, which is a ST recently associated with enterotoxigenic E. coli (ETEC) causing diarrhea . This might point towards fly pollution through stool-contaminated surfaces, possibly through a common source. However, note that we did not detect the ETEC-defining heat-labile and/or heat-stable toxins. Our phylogenetic analysis suggested clonality among our five ST5474 strains (1–9 SNPs/aligned Mbp), and similarity to five publicly available ST5474 genomes (178–560 SNPs/aligned Mbp) (Figure S2).
Three E. coli strains (PBIO1939, PBIO1940 and PBIO1941), which did not only originate from individual flies captured in different wards but belonged to two different clonal lineages (ST410 and ST617), carried similar resistance genes (Table S1), however they differed in their overall plasmid content (Fig. 1c).
The two P. aeruginosa genomes contained several previously described virulence features mandatory for severe invasive infections including flagella, the type III secretion system, type IV pili, as well as toxins and proteases. The A. baumannii genome carried virulence genes associated with serum survival and invasion (phospholipase PLC) (Table S1). Overall, all analyzed genomes showed high virulence potentials (Fig. 1b).
Our results demonstrate that half of the flies in this tertiary hospital in Rwanda carried virulent MRGN pathogens including the pathogenic clonal E. coli lineage ST131. High pre-admission and even higher discharge rates at this facility  may suggest that a) patients and caregivers were the source of MRGN for the flies and b) that flies play a role in the transmission of antimicrobial-resistant pathogens within clinics and in mirroring the burden of antimicrobial resistance  at that time. Even though the actual transmission of MRGN bacteria through flies to humans awaits verification, respective modelling results point strongly into this direction .
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We thank Torsten Semmler (Robert Koch Institute, Berlin, Germany) and Sebastian Guenther (University of Greifswald, Greifswald, Germany) for their support during the initial sequence analysis.
Investigations in Rwanda were supported by the German Federal Ministry for Economic Cooperation and Development via the ESTHER programme (Ensemble pour une Solidarité Thérapeutique Hospitalière En Réseau). We acknowledge support for the Article Processing Charge from the DFG (German Research Foundation, 393148499) and the Open Access Publication Fund of the University of Greifswald.
Authors and Affiliations
Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Str. 17, 17489, Greifswald, Germany
Stefan E. Heiden, Elias Eger & Katharina Schaufler
KS and FPM designed and drafted the manuscript. Experiments were performed by SEH, EE and MSEK. JB, CB, JMN, AS and JBG helped analyzing the results. JB, CB, JMN, AS and JBG helped in proofreading and editing of the manuscript. All authors read and approved the final manuscript.
Phylogenomic tree of five E. coli sequence type (ST) 5474 fly isolates (strain names colored according to Fig. 1c) and publicaly available WGS data of five ST5474 strains (raw read accession nos.; black).
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Heiden, S.E., Kurz, M.S.E., Bohnert, J. et al. Flies from a tertiary hospital in Rwanda carry multidrug-resistant Gram-negative pathogens including extended-spectrum beta-lactamase-producing E. coli sequence type 131.
Antimicrob Resist Infect Control9, 34 (2020). https://doi.org/10.1186/s13756-020-0696-y