Fourteen mcr-1-Positive Salmonella enterica Isolates Recovered from Travelers Returning to the United States from the Dominican Republic.

In the United States, reports of Salmonella enterica carrying mcr-1 remain rare in humans, but when observed, the infection is often associated with travel. Here, we report 14 mcr-1-positive Salmonella enterica isolates from patients in the United States that reported travel to the Dominican Republic within the 12 months before illness.

ANNOUNCEMENT

Colistin is a last resort treatment for multidrug-resistant (MDR) infections. The most common mobile colistin resistance gene mcr-1 was first reported in Enterobacteriaceae in 2015 and has since been observed globally, carried by several plasmid types (1, 2). In the United States, where colistin has not been approved for growth promotion in food-animal production, mcr-1 remains rare in enteric pathogens isolated from humans. When observed, it is often associated with international travel before illness onset, suggesting acquisition outside the United States (3). We report all mcr-1-positive nontyphoidal Salmonella sp. collected from U.S. patients reporting travel to the Dominican Republic (DR) from 2016 to 2021.

Since 2015, state public health laboratories routinely perform whole-genome sequencing of enteric pathogen isolates and, occasionally, older special interest isolates (4). We screened sequenced isolates collected from 2008 to 2021 for resistance determinants using either ResFinder (90% identity, 50% coverage) and the Salmonella PointFinder scheme implemented in staramr v0.4.0 (https://github.com/phac-nml/staramr) or Pathogen Detection (https://www.ncbi.nlm.nih.gov/pathogen). Patients with an mcr-1-positive isolate were interviewed for clinical and epidemiologic information, including demographics, hospitalization, and travel history. Fourteen patients with an mcr-1-positive isolate reported travel to DR, of which 11 reported illness onset during travel or within 7 days of return, 2 reported illness at 4 to 5 months posttravel, and 1 did not have travel and illness onset date available. Genomic DNA was extracted with the Wizard genomic DNA purification kit (using a modified manufacturer’s protocol; Promega, WI) from 12/14 mcr-1-positive isolates incubated on tryptic soy agar-sheep blood at 37°C overnight. Libraries were prepared using the rapid barcoding kit (manufacturer’s protocol; SQK-RBK004; Oxford Nanopore Technologies, Oxford, UK) and sequenced for 72 hours on a GridION instrument using R9.4.1 flow cells (default parameters; Oxford Nanopore Technologies). Reads were base called, filtered, and assembled, and drafted assemblies were polished using an internal workflow (https://github.com/kapsakcj/nanoporeWorkflow; v0.5.0) including Guppy v4.2.2, Filtlong v0.2.0 (https://github.com/rrwick/Filtlong), Flye v2.7 (5), Racon v1.3.1 (6), and Medaka v1.2.0 (https://github.com/nanoporetech/medaka). Isolates that failed to generate circular contigs by this method were hybrid assembled with Unicycler v0.4.8 default parameters (7) using corresponding reads from the NCBI Sequence Read Archive. Mobile genetic elements were identified using Galileo AMR (https://galileoamr.arcbio.com/mara/).

Despite the mcr-1 gene occurring in two different Salmonella enterica serotypes (Enteritidis and Infantis) and over a 6-year time span, the mcr-1 gene is carried on highly related (99.9% identity) ∼33-kb IncX4 plasmids (Table 1); one IncX4 plasmid also carries mph(A) in an 11,269-bp transposon (5-bp direct repeats) (Fig. 1). Two previously sequenced Escherichia coli isolates (GenBank CP018773.2 [8] and CP019908.1) from U.S. patients with DR travel history also carry this IncX4-mcr-1 plasmid (>99% identity), indicating its presence in other Enterobacteriaceae in the DR. Of interest, the Salmonella Infantis isolates reported here carry the large poultry-associated pESI-like MDR plasmid (9–11), suggesting a possible poultry reservoir for IncX4-mcr-1 plasmids. The findings of this report may underrepresent mcr-1-positive Salmonella in humans reporting travel to the DR, as complete travel histories and sequencing data are not always available. Further work to elucidate the extent of mcr-1 dissemination, potential sources, and the risk for human exposure could include testing throughout chicken production in the DR.

TABLE 1

Summary information for the 14 mcr-1-positive Salmonella enterica isolates collected from patients reporting travel to the Dominican Republic

Strain	BioSample NCBI accession no.	SRA NCBI accession no.	GenBank NCBI accession no.	Mean read length	No. of reads	No. of contigs	Read N50 (bp)	Contig N50 (bp)	Genome GC content (%)	Total size (bp)	Assembly method	Serotype	Collection yr	Resistance determinants	Plasmid replicon(s)
2016AM-3354	SAMN07561517	SRR5978786	CP092290, CP092291, CP092292, CP092293	5,702.7	104,437	4	12,734	4,685,559	52.04	4,847,253	Nanopore WFv0.5.0	Enteritidis	2016	gyrA(D87N), mcr-1.1	IncFII(S), IncFIB(S), IncX4
PNUSAS006351	SAMN06183523	SRR5129179	CP092329, CP092330, CP092331	7,773.3	332,055	3	11,851	4,685,598	52.09	4,778,234	Nanopore WFv0.5.0	Enteritidis	2016	gyrA(D87N), mcr-1.1	IncFIB(S), IncFII(S), IncX4
PNUSAS011707	SAMN06842717	SRR5501020	CP092314, CP092315, CP092316, CP092317	3,427.9	55,011	4	8,427	4,685,374	52.00	4,796,200	Nanopore WFv0.5.0	Enteritidis	2017	floR, gyrA(D87N), mcr-1.1, tet(A)	IncX4, IncFII(pCRY), IncX1
PNUSAS019263	SAMN07411119	SRR5888036	CP092318, CP092319, CP092320	3,976.6	120,531	3	9,465	4,685,139	52.09	4,836,993	Nanopore WFv0.5.0	Enteritidis	2017	gyrA(D87N), mcr-1.1	IncFII(S), IncFIB(S), IncX4
PNUSAS020468	SAMN07615603	SRR6039014	CP092310, CP092311, CP092312, CP092313	3,558.1	85,220	4	7,364	4,685,470	52.06	4,864,698	Nanopore WFv0.5.0	Enteritidis	2017	gyrA(D87N), mcr-1.1	IncFIB(S), IncFII(S), IncI1-I(gamma), IncX4
PNUSAS020938	SAMN07554667	SRR5988440	CP092326, CP092327, CP092328	2,641.4	79,614	3	8,590	4,685,443	52.09	4,778,094	Nanopore WFv0.5.0	Enteritidis	2017	gyrA(D87N), mcr-1.1	IncFII(S), IncFIB(S), IncX4
PNUSAS034908	SAMN08773116	SRR6879554	CP092321, CP092322, CP092323, CP092324, CP092325	3,556.9	564,682	5	6,532	4,685,324	52.02	4,911,536	Nanopore WFv0.5.0	Enteritidis	2018	blaCMY-2, gyrA(D87N), mcr-1.1	IncI1-I(gamma), IncFIB(S), IncFII(S), IncX4
PNUSAS037276	SAMN08885897	SRR6955992	CP092307, CP092308, CP092309	3,795.7	63,499	3	8,419	4,685,597	52.09	4,778,225	Nanopore WFv0.5.0	Enteritidis	2018	gyrA(D87N), mcr-1.1	IncFII(S), IncFIB(S), IncX4
PNUSAS070846	SAMN11178030	SRR8756606	CP092304, CP092305, CP092306	3,940.4	63,082	3	11,528	4,683,067	52.10	4,775,722	Nanopore WFv0.5.0	Enteritidis	2019	gyrA(D87N), mcr-1.1	IncX4, IncFIB(S), IncFII(S)
PNUSAS224836a	SAMN21171963	SRR15687865	GCA_019850745.1	148.6	908,906	35	NA	476,570	51.99	4,838,548	SKESA v2.2	Enteritidis	2021	gyrA(D87Y), mcr-1.1	IncX4
PNUSAS238936a	SAMN22561277	SRR16563833	GCA_020611275.1	240.6	830,043	32	NA	406,326	52.01	4,797,053	SKESA v2.2	Enteritidis	2021	gyrA(D87Y), mcr-1.1	IncFIB(S), IncX4, IncFII(S), ColpVC
PNUSAS041145	SAMN09260921	SRR7218560	CP092297, CP092298, CP092299, CP092300	8,101.8	135,232	4	13,420	4,727,179	52.04	5,181,013	Unicycler hybrid	Infantis	2018	aac(3)-IV, ant(3'')-Ia, aph(3')-Ia, aph(4)-Ia, blaCMY-2, blaCTX-M-65, dfrA14, floR, fosA3, gyrA(D87Y), mcr-1.1, sul1, tet(A)	IncX4, IncFIB(pN55391), IncI1-I(gamma)
PNUSAS047891	SAMN09761678	SRR7639227	CP092301, CP092302, CP092303	8,322.2	145,156	3	13,321	4,727,148	52.10	5,094,232	Unicycler hybrid	Infantis	2018	aac(3)-IV, ant(3'')-Ia, aph(3')-Ia, aph(4)-Ia, blaCTX-M-65, dfrA14, floR, fosA3, gyrA(D87Y), mcr-1.1, mph(A), sul1, tet(A)	IncX4, IncFIB(pN55391)
PNUSAS070160	SAMN11178028	SRR8756596	CP092294, CP092295, CP092296	4,396.0	143,706	3	11,367	4,726,980	52.09	5,082,785	Unicycler hybrid	Infantis	2019	aac(3)-IV, ant(3'')-Ia, aph(3')-Ia, aph(4)-Ia, blaCTX-M-65, dfrA14, floR, fosA3, gyrA(D87Y), mcr-1.1, sul1, tet(A)	IncX4, IncFIB(pN55391)

Only the short-read assembly was reported (n = 2); isolates were not available for long-read sequencing.

FIG 1

Mauve alignment of 16 mcr-1-positive IncX4 plasmids, namely, 14 reported here in Salmonella and 2 from previously sequenced Escherichia coli (CP018773 [8] and CP019908). All isolates were collected from patients in the United States that reported travel to the Dominican Republic. Resistance genes, mobile genetic elements, and direct repeats are annotated with colored arrows. Each vertical black line represents a single mutation. The figure was created in Geneious Prime.

Data availability.

The sequences discussed here have been deposited in GenBank and SRA under the accession and BioSample numbers listed in Table 1.