Literature DB >> 32703838

Examination of 189 Campylobacter Species Isolates from the Global Enteric Multicenter Study.

Riley G Risteen^1,2, Tracy H Hazen^1,2, Jane M Michalski^1,2, Frédéric Poly³, Sharon M Tennant^2,4, David A Rasko^5,2.

Abstract

We have examined the draft genomes of 189 Campylobacter species isolates from the Global Enteric Multicenter Study, in which Campylobacter species were identified as significant pathogens.

Entities: CellLine Chemical Disease Species

Year: 2020 PMID： 32703838 PMCID： PMC7378037 DOI： 10.1128/MRA.00646-20

Source DB: PubMed Journal: Microbiol Resour Announc ISSN： 2576-098X

ANNOUNCEMENT

Diarrheal disease is one of the most significant causes of morbidity and death in lower- and middle-income countries (1, 2). The Global Enteric Multicenter Study (GEMS), a prospective case-control study unprecedented in scale, was undertaken to examine the causes of acute moderate-to-severe diarrhea in children under the age of 5 years at seven sites in Africa and Asia (3, 4). The Campylobacter species isolates were cultured as described previously (5). Briefly, Campylobacter species were identified by plating diluted stool onto Campylobacter blood agar plates overnight at 37°C. Single colonies were examined, and those that were catalase and oxidase positive were examined microscopically for small Gram-negative rods that were slightly curved or S-shaped. A total of 189 Campylobacter species isolates were examined by whole-genome sequencing (Table 1). In this submission, we have sequenced 35 isolates of Campylobacter coli, 3 isolates of Campylobacter lari, and 151 isolates of Campylobacter jejuni. These isolates represent a selection of isolates from both cases and controls from each of the seven sites of the GEMS.

TABLE 1

Genome statistics

Sample	Species	Country of origin	No. of reads	No. of bases sequenced	Genome coverage (×)	No. of contigs	Size (bp)	GC content (%)	N₅₀ (bp)	Whole-genome sequence accession no.	SRA accession no.
100179	Campylobacter jejuni	Gambia	6,203,710	936,760,210	540.5	38	1,733,171	30.47	286,964	JAAJZR000000000	SRR11268331
100854	Campylobacter jejuni	Gambia	8,906,498	1,344,881,198	789.3	42	1,703,935	30.55	176,129	JAAJZQ000000000	SRR11268330
102163	Campylobacter jejuni	Gambia	15,812,146	2,387,634,046	1,436.9	41	1,661,608	30.8	157,957	JAAJZP000000000	SRR11268329
102389	Campylobacter jejuni	Gambia	7,434,154	1,122,557,254	642.5	46	1,747,259	30.47	219,778	JAAJZO000000000	SRR11268327
102405	Campylobacter jejuni	Gambia	4,066,296	614,010,696	362.8	37	1,692,235	30.28	118,378	JAAJZN000000000	SRR11268326
102406	Campylobacter jejuni	Gambia	4,778,384	721,535,984	423.4	41	1,704,044	30.34	154,532	JAAJZM000000000	SRR11268325
102470	Campylobacter jejuni	Gambia	7,069,274	1,067,460,374	662.3	35	1,611,762	30.68	181,371	JAAJZL000000000	SRR11268324
102495	Campylobacter jejuni	Gambia	3,337,740	503,998,740	297.1	39	1,696,560	30.27	117,403	JAAJZK000000000	SRR11268323
102500	Campylobacter jejuni	Gambia	6,173,594	932,212,694	581.6	23	1,602,957	30.48	298,201	JAAJZJ000000000	SRR11268322
102624	Campylobacter jejuni	Gambia	5,794,162	874,918,462	468.3	57	1,868,440	31.53	154,560	JAAJZI000000000	SRR11268321
102796	Campylobacter jejuni	Gambia	4,272,412	645,134,212	374.1	31	1,724,717	30.29	181,874	JAAJZH000000000	SRR11268320
102808	Campylobacter jejuni	Gambia	6,356,930	959,896,430	558.2	24	1,719,584	30.29	286,960	JAAJZG000000000	SRR11268319
102878	Campylobacter jejuni	Gambia	5,740,342	866,791,642	498.0	36	1,740,422	30.26	154,555	JAAJZF000000000	SRR11268318
102879	Campylobacter jejuni	Gambia	5,483,538	828,014,238	447.6	144	1,849,863	30.21	37,456	JAAJZE000000000	SRR11268316
102895	Campylobacter jejuni	Gambia	5,547,986	837,745,886	474.9	47	1,763,939	30.13	175,306	JAAJZD000000000	SRR11268315
102920	Campylobacter jejuni	Gambia	4,479,356	676,382,756	404.8	33	1,670,818	30.27	179,731	JAAJZC000000000	SRR11268314
102928	Campylobacter jejuni	Gambia	6,007,354	907,110,454	523.7	49	1,732,203	30.29	126,828	JAAJZB000000000	SRR11268313
102930	Campylobacter jejuni	Gambia	5,696,706	860,202,606	499.9	34	1,720,905	30.29	181,871	JAAJZA000000000	SRR11268312
102954	Campylobacter jejuni	Gambia	5,149,276	777,540,676	448.0	47	1,735,550	30.29	119,613	JAAJYZ000000000	SRR11268311
102958	Campylobacter jejuni	Gambia	4,729,804	714,200,404	413.5	21	1,727,062	30.27	286,964	JAAJYY000000000	SRR11268310
103022	Campylobacter jejuni	Gambia	6,206,532	937,186,332	561.7	37	1,668,488	30.28	179,745	JAAJYX000000000	SRR11268309
103067	Campylobacter jejuni	Gambia	4,389,078	662,750,778	376.0	43	1,762,822	30.14	260,015	JAAJYW000000000	SRR11268308
103092	Campylobacter jejuni	Gambia	4,759,248	718,646,448	419.3	32	1,713,942	30.2	179,602	JAAJYV000000000	SRR11268307
103169	Campylobacter jejuni	Gambia	4,669,524	705,098,124	409.6	27	1,721,614	30.29	290,964	JAAJYU000000000	SRR11268305
103223	Campylobacter jejuni	Gambia	5,748,660	868,047,660	492.4	45	1,763,047	30.14	183,776	JAAJYT000000000	SRR11268304
103290	Campylobacter jejuni	Gambia	4,386,094	662,300,194	385.9	24	1,716,368	30.26	154,555	JAAJYS000000000	SRR11268303
103392	Campylobacter jejuni	Gambia	3,276,204	494,706,804	293.6	26	1,685,246	30.27	178,894	JAAJYR000000000	SRR11268302
120722	Campylobacter jejuni	Gambia	6,315,044	953,571,644	590.9	25	1,613,725	30.52	151,343	JAAJYQ000000000	SRR11268301
201108	Campylobacter coli	Mali	7,545,542	1,139,376,842	667.0	37	1,708,305	31.53	220,782	JAAKBA000000000	SRR11268291
202143	Campylobacter jejuni	Mali	7,256,954	1,095,800,054	625.5	34	1,751,776	30.19	179,603	JAAJYP000000000	SRR11268300
202370	Campylobacter jejuni	Mali	7,754,042	1,170,860,342	652.1	38	1,795,460	30.42	227,186	JAAJYO000000000	SRR11268299
202376	Campylobacter jejuni	Mali	7,148,482	1,079,420,782	670.1	14	1,610,873	30.51	289,842	JAAJYN000000000	SRR11268298
202388	Campylobacter jejuni	Mali	7,688,784	1,161,006,384	676.1	43	1,717,214	30.52	188,083	JAAJYM000000000	SRR11268297
202648	Campylobacter jejuni	Mali	7,446,846	1,124,473,746	644.3	28	1,745,343	30.2	221,009	JAAJYL000000000	SRR11268296
202813	Campylobacter jejuni	Mali	7,559,292	1,141,453,092	642.9	43	1,775,560	30.41	179,602	JAAJYK000000000	SRR11268294
202823	Campylobacter coli	Mali	7,093,986	1,071,191,886	621.3	85	1,724,140	31.5	38,132	JAAKAZ000000000	SRR11268290
202982	Campylobacter coli	Mali	7,647,166	1,154,722,066	636.7	181	1,813,673	31.43	24,698	JAAKAY000000000	SRR11268270
203005	Campylobacter coli	Mali	7,203,060	1,087,662,060	630.5	29	1,725,153	31.56	228,869	JAAKAX000000000	SRR11268259
203008	Campylobacter coli	Mali	6,361,554	960,594,654	550.2	36	1,745,999	31.46	135,201	JAAKAW000000000	SRR11268328
203010	Campylobacter coli	Mali	6,071,568	916,806,768	513.0	139	1,787,086	31.96	33,582	JAAKAV000000000	SRR11268317
203047	Campylobacter jejuni	Mali	8,280,092	1,250,293,892	720.9	87	1,734,318	30.69	66,924	JAAJYJ000000000	SRR11268293
203061	Campylobacter jejuni	Mali	7,907,742	1,194,069,042	717.5	67	1,664,323	30.69	74,708	JAAJYI000000000	SRR11268292
203065	Campylobacter jejuni	Mali	6,275,160	947,549,160	539.9	51	1,755,162	30.43	179,754	JAAJYH000000000	SRR11268209
203086	Campylobacter jejuni	Mali	7,593,766	1,146,658,666	690.7	31	1,660,160	30.62	167,636	JAAJYG000000000	SRR11268208
203109	Campylobacter coli	Mali	5,126,262	774,065,562	448.7	37	1,724,961	31.52	217,565	JAAKAU000000000	SRR11268306
203122	Campylobacter jejuni	Mali	5,595,104	844,860,704	494.7	19	1,707,883	30.36	154,544	JAAJYF000000000	SRR11268207
203138	Campylobacter coli	Mali	6,718,906	1,014,554,806	594.1	20	1,707,836	31.31	218,038	JAAKAT000000000	SRR11268295
203174	Campylobacter jejuni	Mali	6,560,894	990,694,994	596.4	24	1,661,016	30.65	288,875	JAAJYE000000000	SRR11268206
203196	Campylobacter jejuni	Mali	4,312,172	651,137,972	377.3	45	1,725,848	30.18	116,451	JAAJYD000000000	SRR11268205
203266	Campylobacter jejuni	Mali	9,282,290	1,401,625,790	776.6	62	1,804,710	30.93	148,393	JAAJYC000000000	SRR11268204
203429	Campylobacter jejuni	Mali	7,183,880	1,084,765,880	624.7	107	1,736,430	30.93	40,389	JAAJYB000000000	SRR11268203
203531	Campylobacter jejuni	Mali	6,471,590	977,210,090	590.4	26	1,655,127	30.42	151,233	JAAJYA000000000	SRR11268201
203542	Campylobacter jejuni	Mali	6,579,938	993,570,638	584.7	42	1,699,349	30.53	140,624	JAAJXZ000000000	SRR11268200
203645	Campylobacter coli	Mali	8,250,328	1,245,799,528	737.2	51	1,689,940	31.62	111,902	JAAKAS000000000	SRR11268202
203720	Campylobacter jejuni	Mali	6,627,054	1,000,685,154	588.4	19	1,700,696	30.26	188,108	JAAJXY000000000	SRR11268199
203813	Campylobacter jejuni	Mali	4,344,186	655,972,086	365.0	47	1,797,234	30.13	188,749	JAAJXX000000000	SRR11268198
203873	Campylobacter coli	Mali	3,742,778	565,159,478	335.0	21	1,686,902	31.31	163,658	JAAKAR000000000	SRR11268175
203875	Campylobacter jejuni	Mali	4,140,734	625,250,834	354.8	48	1,762,279	30.15	154,426	JAAJXW000000000	SRR11268197
203886	Campylobacter jejuni	Mali	7,068,262	1,067,307,562	623.2	26	1,712,631	30.65	329,559	JAAJXV000000000	SRR11268196
203886_2	Campylobacter jejuni	Mali	5,717,342	863,318,642	509.0	14	1,696,040	30.43	327,588	JAAJTZ000000000	SRR11268275
203890	Campylobacter jejuni	Mali	3,193,368	482,198,568	266.9	38	1,806,461	30.13	160,806	JAAJXU000000000	SRR11268195
203927	Campylobacter jejuni	Mali	5,618,672	848,419,472	471.9	218	1,797,735	30.18	20,329	JAAJXT000000000	SRR11268194
203928	Campylobacter coli	Mali	4,261,520	643,489,520	375.5	44	1,713,910	30.2	109,394	JAAJXS000000000	SRR11268177
203953	Campylobacter coli	Mali	7,149,212	1,079,531,012	572.7	78	1,884,894	31.18	131,021	JAAKAQ000000000	SRR11268193
204026	Campylobacter coli	Mali	6,894,468	1,041,064,668	607.4	41	1,714,090	31.69	171,977	JAAKAP000000000	SRR11268182
204028	Campylobacter coli	Mali	7,559,840	1,141,535,840	657.7	135	1,735,644	31.5	32,193	JAAKAO000000000	SRR11268158
204061	Campylobacter jejuni	Mali	5,335,324	805,633,924	460.2	31	1,750,476	30.23	157,758	JAAJXR000000000	SRR11268176
204097	Campylobacter coli	Mali	10,420,228	1,573,454,428	887.7	85	1,772,455	31.21	183,172	JAAJXQ000000000	SRR11268174
204115	Campylobacter jejuni	Mali	5,970,620	901,563,620	511.9	156	1,761,268	31.28	26,471	JAAKAN000000000	SRR11268256
204137	Campylobacter jejuni	Mali	3,680,086	555,692,986	303.8	44	1,828,955	30.15	125,137	JAAJXP000000000	SRR11268173
204171	Campylobacter jejuni	Mali	4,842,366	731,197,266	430.8	13	1,697,378	30.46	220,957	JAAJXO000000000	SRR11268172
204177	Campylobacter jejuni	Mali	4,815,226	727,099,126	428.2	19	1,697,996	30.46	171,489	JAAJXN000000000	SRR11268171
204211	Campylobacter jejuni	Mali	3,415,020	515,668,020	305.0	35	1,690,989	30.44	199,496	JAAJXM000000000	SRR11268170
204252	Campylobacter coli	Mali	4,367,558	659,501,258	398.9	18	1,653,505	30.65	199,497	JAAJXL000000000	SRR11268169
204269	Campylobacter jejuni	Mali	3,676,862	555,206,162	326.0	30	1,703,046	31.34	133,203	JAAKAM000000000	SRR11268245
204304	Campylobacter jejuni	Mali	9,000,690	1,359,104,190	819.1	35	1,659,322	30.92	321,859	JAAJXK000000000	SRR11268168
204332	Campylobacter jejuni	Kenya	4,031,530	608,761,030	359.4	30	1,693,869	30.4	197,610	JAAJXJ000000000	SRR11268167
400636	Campylobacter jejuni	Kenya	7,710,952	1,164,353,752	649.8	46	1,791,802	30.33	230,736	JAAJXI000000000	SRR11268166
400738	Campylobacter jejuni	Kenya	5,121,988	773,420,188	445.3	85	1,736,727	30.23	83,710	JAAJXH000000000	SRR11268165
400745	Campylobacter jejuni	Kenya	4,946,518	746,924,218	432.0	42	1,728,967	30.21	148,462	JAAJXG000000000	SRR11268192
400787	Campylobacter jejuni	Kenya	7,438,370	1,123,193,870	645.7	119	1,739,435	30.46	29,731	JAAJXF000000000	SRR11268191
400797	Campylobacter jejuni	Kenya	6,124,418	924,787,118	544.7	40	1,697,839	30.49	139,022	JAAJXE000000000	SRR11268190
401051	Campylobacter jejuni	Kenya	3,314,158	500,437,858	293.5	36	1,705,014	30.23	179,526	JAAJXD000000000	SRR11268189
401125	Campylobacter jejuni	Kenya	4,314,926	651,553,826	386.9	32	1,684,238	30.22	293,998	JAAJXC000000000	SRR11268188
401207	Campylobacter jejuni	Kenya	7,113,334	1,074,113,434	634.6	34	1,692,512	30.29	140,280	JAAJXB000000000	SRR11268187
401272	Campylobacter jejuni	Kenya	4,766,168	719,691,368	425.0	30	1,693,542	30.31	170,153	JAAJXA000000000	SRR11268186
401419	Campylobacter jejuni	Kenya	9,693,016	1,463,645,416	840.1	63	1,742,226	30.75	153,642	JAAJWZ000000000	SRR11268185
401554	Campylobacter jejuni	Kenya	4,126,962	623,171,262	369.6	27	1,685,911	30.28	148,420	JAAJWY000000000	SRR11268184
402330	Campylobacter jejuni	Kenya	7,350,650	1,109,948,150	657.6	28	1,687,804	30.54	291,465	JAAJWX000000000	SRR11268183
402665	Campylobacter jejuni	Kenya	3,394,254	512,532,354	302.0	27	1,696,910	30.2	224,886	JAAJWW000000000	SRR11268181
402692	Campylobacter jejuni	Kenya	4,168,684	629,471,284	357.8	46	1,759,362	30.15	119,983	JAAJWV000000000	SRR11268180
402718	Campylobacter jejuni	Kenya	7,688,018	1,160,890,718	675.0	84	1,719,910	30.5	66,365	JAAJWU000000000	SRR11268179
402747	Campylobacter jejuni	Kenya	4,463,534	673,993,634	392.8	25	1,715,706	30.25	154,554	JAAJWT000000000	SRR11268178
402930	Campylobacter jejuni	Kenya	4,735,142	715,006,442	433.3	11	1,650,263	30.5	181,931	JAAJWS000000000	SRR11268164
403073	Campylobacter coli	Kenya	3,330,874	502,961,974	313.6	25	1,603,818	30.55	189,338	JAAKBC000000000	SRR11268234
403107	Campylobacter jejuni	Kenya	1,668,904	252,004,504	152.1	26	1,657,349	31.36	141,482	JAAKAL000000000	SRR11268223
403132	Campylobacter jejuni	Kenya	4,606,780	695,623,780	411.1	52	1,692,195	30.27	110,293	JAAJWR000000000	SRR11268163
403138	Campylobacter jejuni	Kenya	4,837,712	730,494,512	436.3	28	1,674,409	30.34	291,943	JAAJWQ000000000	SRR11268162
403205	Campylobacter jejuni	Kenya	4,879,426	736,793,326	457.2	20	1,611,600	30.43	180,161	JAAJWP000000000	SRR11268161
403259	Campylobacter jejuni	Kenya	5,342,188	806,670,388	502.1	42	1,606,710	30.47	141,357	JAAJWO000000000	SRR11268160
403459	Campylobacter jejuni	Kenya	5,669,500	856,094,500	499.7	161	1,713,238	30.29	30,234	JAAJWN000000000	SRR11268159
403772	Campylobacter jejuni	Kenya	5,181,170	782,356,670	424.8	78	1,841,742	31.9	109,555	JAAJWM000000000	SRR11268157
403834	Campylobacter jejuni	India	6,305,490	952,128,990	549.9	26	1,731,379	30.22	189,394	JAAJWL000000000	SRR11268156
500153	Campylobacter jejuni	India	6,803,370	1,027,308,870	570.7	44	1,800,234	30.42	179,937	JAAJWK000000000	SRR11268155
500213	Campylobacter jejuni	India	5,345,888	807,229,088	494.3	19	1,633,002	30.63	296,986	JAAJWJ000000000	SRR11268154
500215	Campylobacter jejuni	India	6,673,956	1,007,767,356	603.0	40	1,671,227	30.69	184,448	JAAJWI000000000	SRR11268153
500340	Campylobacter jejuni	India	6,408,974	967,755,074	533.7	71	1,813,151	30.7	129,061	JAAJWH000000000	SRR11268152
500380	Campylobacter jejuni	India	6,333,678	956,385,378	548.6	36	1,743,323	30.36	157,821	JAAJWG000000000	SRR11268340
500400	Campylobacter jejuni	India	7,287,656	1,100,436,056	609.8	65	1,804,682	30.86	183,643	JAAJWF000000000	SRR11268339
500435	Campylobacter jejuni	India	5,905,760	891,769,760	487.3	33	1,830,172	30.13	155,314	JAAJWE000000000	SRR11268338
500438	Campylobacter jejuni	India	5,402,998	815,852,698	496.1	26	1,644,604	30.52	195,816	JAAJWD000000000	SRR11268257
500461	Campylobacter jejuni	India	9,498,782	1,434,316,082	816.2	47	1,757,345	30.67	169,666	JAAKBB000000000	SRR11268212
500480	Campylobacter jejuni	India	5,512,630	832,407,130	485.0	44	1,716,146	30.33	183,127	JAAJWC000000000	SRR11268255
500481	Campylobacter jejuni	India	4,762,896	719,197,296	422.4	24	1,702,587	30.26	179,580	JAAJWB000000000	SRR11268254
500496	Campylobacter jejuni	India	4,474,008	675,575,208	420.6	18	1,606,157	30.46	185,577	JAAJWA000000000	SRR11268253
500499	Campylobacter jejuni	India	4,306,534	650,286,634	405.1	22	1,605,363	30.46	289,666	JAAJVZ000000000	SRR11268252
500563	Campylobacter jejuni	India	3,799,978	573,796,678	326.7	26	1,756,195	30.33	183,645	JAAJVY000000000	SRR11268251
500570	Campylobacter jejuni	India	3,790,534	572,370,634	306.9	52	1,865,128	29.94	135,995	JAAJVX000000000	SRR11268250
500591	Campylobacter jejuni	India	3,856,054	582,264,154	340.1	50	1,712,101	30.21	106,391	JAAJVW000000000	SRR11268249
500592	Campylobacter jejuni	India	3,250,106	490,766,006	280.9	28	1,746,970	30.33	183,643	JAAJVV000000000	SRR11268248
500656	Campylobacter jejuni	India	4,044,558	610,728,258	361.0	21	1,691,876	30.33	197,545	JAAJVU000000000	SRR11268247
500704	Campylobacter jejuni	India	5,176,274	781,617,374	466.3	22	1,676,235	30.28	286,518	JAAJVT000000000	SRR11268246
500708	Campylobacter jejuni	India	4,080,866	616,210,766	348.8	25	1,766,601	30.23	185,888	JAAJVS000000000	SRR11268244
500710	Campylobacter lari	India	5,000,046	755,006,946	446.5	18	1,690,895	30.33	286,415	JAAJVR000000000	SRR11268243
503734	Campylobacter jejuni	India	6,220,854	939,348,954	638.7	37	1,470,770	29.98	127,023	JAAJTY000000000	SRR11268274
503824	Campylobacter jejuni	India	6,596,446	996,063,346	586.0	31	1,699,640	30.49	183,845	JAAJVQ000000000	SRR11268242
504218	Campylobacter lari	India	6,764,224	1,021,397,824	666.9	51	1,531,487	30.01	142,803	JAAJTX000000000	SRR11268273
504478	Campylobacter lari	India	6,995,424	1,056,309,024	707.3	37	1,493,515	29.9	143,751	JAAJTW000000000	SRR11268272
504557	Campylobacter jejuni	India	5,937,750	896,600,250	520.6	171	1,722,124	30.53	24,430	JAAJVP000000000	SRR11268241
504611	Campylobacter jejuni	India	4,722,690	713,126,190	420.1	38	1,697,648	30.22	180,012	JAAJVO000000000	SRR11268240
504764	Campylobacter jejuni	India	4,280,046	646,286,946	362.6	42	1,782,268	30.19	180,046	JAAJVN000000000	SRR11268239
510942	Campylobacter jejuni	India	5,613,382	847,620,682	487.6	33	1,738,188	30.33	148,210	JAAJVM000000000	SRR11268238
511171	Campylobacter jejuni	India	3,872,784	584,790,384	336.9	67	1,735,885	30.18	128,079	JAAJVL000000000	SRR11268237
521136	Campylobacter jejuni	India	5,597,404	845,208,004	525.7	20	1,607,829	30.47	289,690	JAAJVK000000000	SRR11268236
521162	Campylobacter jejuni	India	5,551,710	838,308,210	478.2	70	1,752,915	30.27	64,603	JAAJVJ000000000	SRR11268235
600001	Campylobacter coli	Bangladesh	6,716,828	1,014,241,028	558.0	72	1,817,597	31.57	163,114	JAAKAK000000000	SRR11268281
600030	Campylobacter jejuni	Bangladesh	6,103,334	921,603,434	520.9	111	1,769,377	31.57	32,279	JAAKAJ000000000	SRR11268271
600032	Campylobacter jejuni	Bangladesh	7,212,888	1,089,146,088	593.8	59	1,834,224	30.39	174,893	JAAJVI000000000	SRR11268233
600034	Campylobacter jejuni	Bangladesh	8,838,754	1,334,651,854	755.6	92	1,766,375	30.53	52,978	JAAJVH000000000	SRR11268232
600099	Campylobacter jejuni	Bangladesh	4,802,490	725,175,990	436.5	16	1,661,406	30.46	153,905	JAAJVG000000000	SRR11268231
600883	Campylobacter jejuni	Bangladesh	5,279,702	797,235,002	459.6	32	1,734,451	30.23	119,457	JAAJVF000000000	SRR11268230
600978	Campylobacter jejuni	Bangladesh	3,440,852	519,568,652	293.2	44	1,772,006	30.21	158,690	JAAJVE000000000	SRR11268229
601037	Campylobacter jejuni	Bangladesh	7,135,232	1,077,420,032	644.4	23	1,671,899	30.38	129,032	JAAJVD000000000	SRR11268228
602950	Campylobacter jejuni	Bangladesh	6,987,878	1,055,169,578	644.2	90	1,638,017	30.61	39,830	JAAJVC000000000	SRR11268227
603180	Campylobacter jejuni	Bangladesh	6,059,946	915,051,846	531.1	48	1,723,063	30.38	103,103	JAAJVB000000000	SRR11268226
603771	Campylobacter jejuni	Bangladesh	2,884,482	435,556,782	260.9	36	1,669,130	30.32	217,195	JAAJVA000000000	SRR11268225
604313	Campylobacter coli	Bangladesh	4,858,970	733,704,470	391.7	83	1,872,995	30.07	64,463	JAAJUZ000000000	SRR11268224
604335	Campylobacter coli	Bangladesh	5,029,314	759,426,414	437.5	85	1,735,638	31.25	44,965	JAAKAI000000000	SRR11268269
604349	Campylobacter jejuni	Bangladesh	5,115,372	772,421,172	437.8	52	1,764,238	30.15	120,039	JAAJUY000000000	SRR11268222
604421	Campylobacter jejuni	Bangladesh	4,313,588	651,351,788	403.9	20	1,612,509	30.46	183,854	JAAJUX000000000	SRR11268221
604447	Campylobacter jejuni	Bangladesh	3,836,990	579,385,490	361.0	22	1,605,028	30.47	166,133	JAAJUW000000000	SRR11268220
621131	Campylobacter jejuni	Pakistan	5,314,150	802,436,650	458.0	36	1,752,159	30.27	158,756	JAAJUV000000000	SRR11268219
700462	Campylobacter jejuni	Pakistan	7,264,686	1,096,967,586	621.6	41	1,764,719	30.52	195,884	JAAJUU000000000	SRR11268218
700490	Campylobacter jejuni	Pakistan	6,778,386	1,023,536,286	592.6	34	1,727,095	30.56	183,122	JAAJUT000000000	SRR11268217
700544	Campylobacter coli	Pakistan	6,983,836	1,054,559,236	594.4	35	1,774,282	30.36	183,059	JAAJUS000000000	SRR11268216
703113	Campylobacter coli	Pakistan	8,323,440	1,256,839,440	720.4	35	1,744,622	31.46	162,987	JAAKAH000000000	SRR11268268
703171	Campylobacter coli	Pakistan	5,581,320	842,779,320	471.9	35	1,786,025	31.31	170,264	JAAKAG000000000	SRR11268267
703275	Campylobacter coli	Pakistan	6,374,972	962,620,772	567.9	40	1,694,913	31.58	148,597	JAAKAF000000000	SRR11268266
703313	Campylobacter coli	Pakistan	7,593,126	1,146,562,026	637.2	27	1,799,272	31.38	187,295	JAAKAE000000000	SRR11268265
703452	Campylobacter coli	Pakistan	5,086,318	768,034,018	408.4	170	1,880,625	31.28	25,602	JAAKAD000000000	SRR11268264
703460	Campylobacter jejuni	Pakistan	5,219,202	788,099,502	426.1	55	1,849,671	31.29	78,608	JAAKAC000000000	SRR11268263
703549	Campylobacter jejuni	Pakistan	4,151,542	626,882,842	388.4	20	1,613,952	30.46	183,854	JAAJUR000000000	SRR11268215
703550	Campylobacter jejuni	Pakistan	3,597,594	543,236,694	283.6	46	1,915,743	30.06	141,849	JAAJUQ000000000	SRR11268214
703552	Campylobacter jejuni	Pakistan	5,493,168	829,468,368	429.9	52	1,929,628	30.25	159,911	JAAJUP000000000	SRR11268213
703556	Campylobacter jejuni	Pakistan	1,715,182	258,992,482	160.6	20	1,612,458	30.46	204,239	JAAJUO000000000	SRR11268211
703559	Campylobacter jejuni	Pakistan	4,210,794	635,829,894	375.0	90	1,695,440	30.46	77,683	JAAJUN000000000	SRR11268210
703614	Campylobacter jejuni	Pakistan	5,558,436	839,323,836	476.9	25	1,759,887	30.33	153,853	JAAJUM000000000	SRR11268289
703615	Campylobacter coli	Pakistan	7,414,056	1,119,522,456	631.2	37	1,773,729	30.59	106,560	JAAJUL000000000	SRR11268288
703632	Campylobacter coli	Pakistan	5,720,462	863,789,762	476.6	36	1,812,223	31.29	169,567	JAAKAB000000000	SRR11268262
703637	Campylobacter jejuni	Pakistan	4,708,756	711,022,156	440.7	18	1,613,479	30.46	204,373	JAAJUK000000000	SRR11268287
703638	Campylobacter coli	Pakistan	3,762,142	568,083,442	338.3	66	1,679,162	30.42	108,950	JAAJUJ000000000	SRR11268286
703644	Campylobacter coli	Pakistan	6,563,838	991,139,538	528.8	99	1,874,173	31.94	142,499	JAAKAA000000000	SRR11268261
703646	Campylobacter coli	Pakistan	6,769,006	1,022,119,906	578.1	32	1,768,138	31.43	151,722	JAAJZZ000000000	SRR11268260
703661	Campylobacter jejuni	Pakistan	6,706,838	1,012,732,538	581.2	32	1,742,438	31.44	264,498	JAAJZY000000000	SRR11268258
703664	Campylobacter coli	Pakistan	1,962,430	296,326,930	183.9	33	1,611,531	30.47	118,642	JAAJUI000000000	SRR11268285
703709	Campylobacter coli	Pakistan	6,706,300	1,012,651,300	596.0	28	1,699,150	31.47	220,108	JAAJZX000000000	SRR11268337
703726	Campylobacter coli	Pakistan	8,427,844	1,272,604,444	637.2	147	1,997,094	31.23	56,886	JAAJZW000000000	SRR11268336
703890	Campylobacter jejuni	Pakistan	7,028,076	1,061,239,476	583.0	64	1,820,341	31.43	94,220	JAAJZV000000000	SRR11268335
704017	Campylobacter coli	Pakistan	5,840,460	881,909,460	513.4	31	1,717,949	30.37	173,578	JAAJUH000000000	SRR11268284
704042	Campylobacter jejuni	Pakistan	6,729,102	1,016,094,402	596.2	36	1,704,314	31.52	149,934	JAAJZU000000000	SRR11268334
704082	Campylobacter jejuni	Pakistan	5,120,440	773,186,440	451.2	27	1,713,608	30.32	185,957	JAAJUG000000000	SRR11268283
704083	Campylobacter coli	Pakistan	4,658,208	703,389,408	407.4	34	1,726,402	30.29	179,602	JAAJUF000000000	SRR11268282
704192	Campylobacter coli	Pakistan	7,532,250	1,137,369,750	618.6	55	1,838,551	31.32	117,002	JAAJZT000000000	SRR11268333
704216	Campylobacter jejuni	Pakistan	6,730,994	1,016,380,094	595.3	169	1,707,348	31.68	22,048	JAAJZS000000000	SRR11268332
704227	Campylobacter jejuni	Pakistan	5,271,176	795,947,576	449.1	39	1,772,240	30.33	165,219	JAAJUE000000000	SRR11268280
704230	Campylobacter jejuni	Pakistan	5,598,968	845,444,168	474.7	43	1,781,173	30.13	180,021	JAAJUD000000000	SRR11268279
704264	Campylobacter jejuni	Pakistan	5,665,686	855,518,586	488.8	124	1,750,245	30.19	31,635	JAAJUC000000000	SRR11268278
710603	Campylobacter jejuni	Pakistan	5,812,220	877,645,220	502.1	35	1,747,934	30.18	333,527	JAAJUB000000000	SRR11268277
721225	Campylobacter jejuni	Mali	2,932,018	442,734,718	254.4	30	1,740,017	30.19	155,321	JAAJUA000000000	SRR11268276

Genome statistics Genomic DNA was isolated from cultures grown overnight in lysogeny broth. DNA was extracted in a 96-well format from 100 μl of sample using the MagAttract PowerMicrobiome DNA/RNA kit (Qiagen, Hilden, Germany) automated on a Hamilton Microlab STAR robotic platform. Bead disruption was conducted with a TissueLyser II instrument (20 Hz for 20 min) in a 96-deep-well plate in the presence of 200 μl phenol-chloroform. Genomic DNA was eluted in 90 μl water after magnetic bead cleanup. The resulting genomic DNA was quantified using PicoGreen. The sequencing libraries were generated with the KAPA HyperPrep kit (catalog number KK8504) and sequenced on the Illumina NovaSeq platform using a 150-bp paired-end kit. The total number of reads generated for each isolate is listed in Table 1; values averaged 1,725,208 bp per genome. All software was used with default values. Raw sequencing reads were filtered to remove contaminating PhiX reads using BBDuk of the BBTools software suite (https://sourceforge.net/projects/bbmap). The raw reads were also filtered to remove contaminating Illumina adaptor sequences and quality trimmed using Trimmomatic v.0.36 (6). The resulting filtered reads were then assembled using SPAdes v.3.13.0 (7). The assemblies were filtered to contain only contigs longer than 500 bp with a k-mer coverage of ≥5×. Genomes containing >500 contigs or an aberrant GC content were removed from further analysis. Relevant statistics, including GenBank accession numbers and SRA links for each genome assembly, are included in Table 1. The genomes have a mean sequencing coverage of 505× (standard deviation, 152×; minimum, 152×; maximum, 1,437×). The final assemblies have a mean contig count of 48 (standard deviation, 36 contigs; minimum, 11 contigs; maximum, 218 contigs), a mean genome size of 1,725,208 bp (standard deviation, 73,678 bp; minimum, 1,470,770 bp; maximum, 1,997,094 bp), a mean GC content of 30.6% (standard deviation, 0.48%; minimum, 29.9%; maximum, 32.0%), and a mean N50 value of 161,982 bp (standard deviation, 68,865 bp; minimum, 20,329 bp; maximum, 333,527 bp). Further analysis will reveal the genome dynamics of these important species that cause significant diarrheal disease among humans.

Data availability.

All data have been released, and accession numbers are listed in Table 1.

7 in total

1. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.

Authors: Sergey Nurk; Anton Bankevich; Dmitry Antipov; Alexey A Gurevich; Anton Korobeynikov; Alla Lapidus; Andrey D Prjibelski; Alexey Pyshkin; Alexander Sirotkin; Yakov Sirotkin; Ramunas Stepanauskas; Scott R Clingenpeel; Tanja Woyke; Jeffrey S McLean; Roger Lasken; Glenn Tesler; Max A Alekseyev; Pavel A Pevzner
Journal: J Comput Biol Date: 2013-10 Impact factor: 1.479

2. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study.

Authors: Karen L Kotloff; James P Nataro; William C Blackwelder; Dilruba Nasrin; Tamer H Farag; Sandra Panchalingam; Yukun Wu; Samba O Sow; Dipika Sur; Robert F Breiman; Abu Sg Faruque; Anita Km Zaidi; Debasish Saha; Pedro L Alonso; Boubou Tamboura; Doh Sanogo; Uma Onwuchekwa; Byomkesh Manna; Thandavarayan Ramamurthy; Suman Kanungo; John B Ochieng; Richard Omore; Joseph O Oundo; Anowar Hossain; Sumon K Das; Shahnawaz Ahmed; Shahida Qureshi; Farheen Quadri; Richard A Adegbola; Martin Antonio; M Jahangir Hossain; Adebayo Akinsola; Inacio Mandomando; Tacilta Nhampossa; Sozinho Acácio; Kousick Biswas; Ciara E O'Reilly; Eric D Mintz; Lynette Y Berkeley; Khitam Muhsen; Halvor Sommerfelt; Roy M Robins-Browne; Myron M Levine
Journal: Lancet Date: 2013-05-14 Impact factor: 79.321

3. Diagnostic microbiologic methods in the GEMS-1 case/control study.

Authors: Sandra Panchalingam; Martin Antonio; Anowar Hossain; Inacio Mandomando; Ben Ochieng; Joseph Oundo; T Ramamurthy; Boubou Tamboura; Anita K M Zaidi; William Petri; Eric Houpt; Patrick Murray; Valeria Prado; Roberto Vidal; Duncan Steele; Nancy Strockbine; Philippe Sansonetti; Roger I Glass; Roy M Robins-Browne; Marija Tauschek; Ann-Marie Svennerholm; Lynette Y Berkeley; Karen Kotloff; Myron M Levine; James P Nataro
Journal: Clin Infect Dis Date: 2012-12 Impact factor: 9.079

4. Commentary: Estimates of Global, Regional, and National Morbidity, Mortality, and Aetiologies of Diarrhoeal Diseases: A Systematic Analysis for the Global Burden of Disease Study 2015.

Authors: Amir Abdoli; Nahid Maspi
Journal: Front Med (Lausanne) Date: 2018-01-29

Review 5. Meeting Report: WHO Workshop on modelling global mortality and aetiology estimates of enteric pathogens in children under five. Cape Town, 28-29th November 2018.

Authors: H J Prudden; M Hasso-Agopsowicz; R E Black; C Troeger; R C Reiner; R F Breiman; M Jit; G Kang; L Lamberti; C F Lanata; B A Lopman; W Ndifon; V E Pitzer; J A Platts-Mills; M S Riddle; P G Smith; R Hutubessy; B Giersing
Journal: Vaccine Date: 2020-04-03 Impact factor: 3.641

6. Trimmomatic: a flexible trimmer for Illumina sequence data.

Authors: Anthony M Bolger; Marc Lohse; Bjoern Usadel
Journal: Bioinformatics Date: 2014-04-01 Impact factor: 6.937

7. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study.

Authors: Jie Liu; James A Platts-Mills; Jane Juma; Furqan Kabir; Joseph Nkeze; Catherine Okoi; Darwin J Operario; Jashim Uddin; Shahnawaz Ahmed; Pedro L Alonso; Martin Antonio; Stephen M Becker; William C Blackwelder; Robert F Breiman; Abu S G Faruque; Barry Fields; Jean Gratz; Rashidul Haque; Anowar Hossain; M Jahangir Hossain; Sheikh Jarju; Farah Qamar; Najeeha Talat Iqbal; Brenda Kwambana; Inacio Mandomando; Timothy L McMurry; Caroline Ochieng; John B Ochieng; Melvin Ochieng; Clayton Onyango; Sandra Panchalingam; Adil Kalam; Fatima Aziz; Shahida Qureshi; Thandavarayan Ramamurthy; James H Roberts; Debasish Saha; Samba O Sow; Suzanne E Stroup; Dipika Sur; Boubou Tamboura; Mami Taniuchi; Sharon M Tennant; Deanna Toema; Yukun Wu; Anita Zaidi; James P Nataro; Karen L Kotloff; Myron M Levine; Eric R Houpt
Journal: Lancet Date: 2016-09-24 Impact factor: 79.321

7 in total