Table_2_Genome-Based Analysis of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch (Lates niloticus) of Lake Victoria, Tanzania.XLSX

Extended-spectrum β-lactamase (ESBL)-producing bacteria constitute an emerging global health issue with food products being vehicles of transmission and the aquatic environments serving as potential reservoirs. This study aimed to characterize ESBL-producing Escherichia coli in Nile perch and water from Lake Victoria in Tanzania. A total of 180 samples of Nile perch and 60 water samples were screened for ESBL-producing E. coli on MacConkey agar supplemented with 2 μg/ml of cefotaxime and confirmed by blaCTX–M and blaTEM PCR. Antimicrobial resistance was determined by the disk diffusion method, and the ESBL-producing isolates were whole genome sequencing (WGS). ESBL-producing E. coli were detected in eight of the 180 analyzed Nile perch samples, and only one water sample was positive (1.7%, n = 60). Isolates were resistant to sulfamethoxazole–trimethoprim (100%), ampicillin/cloxacillin (100%), erythromycin 72.7% (8/11), tetracycline 90.9% (10/11), and nalidixic acid 63.6% (7/11). This mostly corroborates the resistance genes that they carried for sulfonamides (sul1 and sul2), trimethoprim (dfrA and dfrB), aminoglycosides [aac(3)-IId, strA, and strB], tetracycline [tet(B) and tet(D)], and fluoroquinolones (qepA4). They harbored plasmid replicon types IncF, IncX, IncQ, and Col and carried blaCTX–M–15 and blaTEM–1B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type–phylogroup–serotype-specific clusters: C1, C2, and C3. Cluster C1 included five strains (3 to 13 SNPs) belonging to ST167, phylogroup A, and serotype O9:H21; the two C2 strains (11 SNPs) belong to ST156, phylogroup B1, and serotype ONT:H28; and C3 was made up of four strains (SNPs ranged from 4 to 17) of ST636, phylogroup B2, and serotype O45:H7. The common virulence gene gad was reported in all strains. In addition, strains in C2 and C3 possessed iss, lpfA, and nfaE virulence genes, and the vat gene was found only in C3. The present study reports the occurrence of multidrug-resistant ESBL-producing E. coli carrying plasmid-mediated ESBL genes in offshore water and Nile perch in Lake Victoria. Strains formed three clonal clusters of unknown origin. This study reveals that the Lake may serve as reservoir for ESBL-producing bacteria that can be transmitted by fish as a food chain hazard of One-Health concern.

产超广谱β-内酰胺酶（Extended-spectrum β-lactamase, ESBL）细菌已成为日益严峻的全球公共卫生问题，食品为其传播载体，水生环境则是潜在的储存宿主。本研究旨在对坦桑尼亚维多利亚湖尼罗河尖吻鲈及湖水样本中产ESBL的大肠埃希菌（Escherichia coli）进行特征分析。共筛选180份尼罗河尖吻鲈样本与60份湖水样本，在添加2 μg/ml头孢噻肟的麦康凯琼脂上分离筛选产ESBL大肠埃希菌，并通过blaCTX–M与blaTEM聚合酶链式反应（PCR）进行确认。采用纸片扩散法测定菌株的抗菌药物耐药性，同时对产ESBL分离株进行全基因组测序（Whole Genome Sequencing, WGS）。在180份分析的尼罗河尖吻鲈样本中检出8份产ESBL大肠埃希菌阳性，60份湖水样本中仅1份阳性（1.7%，n=60）。上述分离株对磺胺甲恶唑-甲氧苄啶（100%）、氨苄西林/氯唑西林（100%）、红霉素（72.7%，8/11）、四环素（90.9%，10/11）及萘啶酸（63.6%，7/11）呈现耐药性。该耐药表型与分离株携带的耐药基因谱基本吻合，包括磺胺类耐药基因sul1、sul2，甲氧苄啶耐药基因dfrA、dfrB，氨基糖苷类耐药基因[aac(3)-IId、strA与strB]，四环素耐药基因[tet(B)与tet(D)]以及氟喹诺酮类耐药基因qepA4。分离株携带IncF、IncX、IncQ及Col型质粒复制子，且blaCTX–M–15与blaTEM–1B基因通常与IncF型质粒复制子位于同一重叠群（contig）上。尽管各菌株在流行病学上无关联，但可划分为3个独立的序列型-系统发育群-血清型特异性克隆簇：C1、C2与C3。C1簇包含5株菌株（单核苷酸多态性差异范围为3~13个），隶属于ST167序列型、系统发育群A及血清型O9:H21；C2簇的2株菌株（单核苷酸多态性差异为11个）隶属于ST156序列型、系统发育群B1及血清型ONT:H28；C3簇由4株菌株组成（单核苷酸多态性差异范围为4~17个），隶属于ST636序列型、系统发育群B2及血清型O45:H7。所有菌株均携带共同毒力基因gad。此外，C2与C3簇菌株还携带iss、lpfA及nfaE毒力基因，vat基因仅存在于C3簇菌株中。本研究报道了维多利亚湖近岸水体及尼罗河尖吻鲈中携带质粒介导ESBL基因的多重耐药产ESBL大肠埃希菌的检出情况。上述菌株形成3个起源未知的克隆簇。本研究揭示，维多利亚湖可作为产ESBL细菌的储存宿主，此类细菌可通过鱼类传播，构成一体化健康（One Health）视角下的食源性公共卫生风险。