Most Domestic Livestock Possess Colistin-Resistant Commensal Escherichia coli Harboring mcr in a Rural Community in Vietnam

LETTER

Colistin is recognized as the last resort for treatment of life-threatening infections caused by multidrug-resistant bacteria; however, the increasing prevalence of colistin-resistant bacteria harboring the mobile colistin resistance (mcr) gene poses a threat to the treatment (1). In this regard, it is considered that the abuse of antibiotic use in the agricultural field may be involved in the emergence and dissemination of antibiotic-resistant bacteria. The current study revealed that more than 70% of the residents in a rural community in Vietnam where colistin-based drugs and colistin-containing feeds were frequently used in livestock breeding (2) retained colistin-resistant Escherichia coli (CR-E) harboring mcr in their fecal microbiota (3). Considering this high level of dissemination of CR-E in the residents, the involvement of backyard breeding livestock, which is common in the area, seems likely. Supporting this notion, we found that most of the backyard livestock in the community carried commensal CR-E harboring mcr. To the best of our knowledge, this is the first report of such an exceptionally high CR-E contamination in livestock.

A total of 72 stool specimens were obtained from backyard livestock, including pigs and chickens, from 41 households in the village of Naguyen Xa, Thai Binh Province, Vietnam, where the CR-E prevalence of the residents was found to be extremely high (3) in August 2018. Rectal swab specimens were collected from the livestock and inoculated onto a selective agar medium (CHROMagar COL-APSE; CHROMagar, Paris, France) for the isolation of colistin-resistant Gram-negative bacteria. One representative E. coli-like colony was isolated and characterized further for bacterial identification, antibiotic susceptibility, colistin resistance genes, and relevance between isolates, as described previously (4–6).

As shown in Table 1, most of the livestock tested showed the presence of CR-E harboring mcr; only 3 animals showed negative results. Differences in the prevalences of CR-E between chickens and pigs were not determined. The MICs of colistin for these isolates was ≥8 mg/liter. In the PCR analysis of colistin resistance genes (mcr-1 to -5) in CR-E isolates, mcr-1 was almost solely detected. There was one exception: an isolate from a pig that carried mcr-3. The susceptibility of CR-E isolates to other antibiotics, including ampicillin, cefoxitin, cefotaxime, ceftazidime, meropenem, streptomycin, kanamycin, gentamicin, ciprofloxacin, nalidixic acid, tetracycline, chloramphenicol, fosfomycin, and sulfamethoxazole-trimethoprim, showed that 95.6% were multidrug resistant, that is, resistant to at least one antibiotic in three or more antibiotic classes (7). The median number of antibiotics showing resistance was 6 (range, 0 to 11). The resistance pattern of these isolates was similar to that of residents from the same community (3) (see Fig. S1 in the supplemental material). No carbapenem-resistant CR-E was detected.

TABLE 1.

Detection of colistin-resistant E. coli harboring mcr in stool specimens of backyard livestock^a

E. coli phenotype or genotype	No. of positive specimens/no. of specimens tested (%)
	All livestock (n = 72)	Chickens (n = 36)	Pigs (n = 36)
Colistin resistant	69/72 (95.8)	35/36 (97.2)	34/36 (94.4)
mcr-1	68/72 (94.4)	35	33
mcr-3	1/72 (1.4)	0	1

^aThe total number of households participating was 41.

Isolate similarity dendrograms assessed by pulsed-gel electrophoresis showed some clonal relationships among isolates of livestock and households (Fig. S2). However, clonal distribution of a certain lineage of CR-E at the livestock population level in the community was not observed.

These data strongly suggest the involvement of backyard livestock microbiota with CR-E in the high prevalence of CR-E in community residents. Therefore, prevention of the spread of antibiotic-resistant bacteria by the concept of One Health is urgently needed (8).